Programming language use distribution from recent programs / articles

-e PMID	LANG	TITLE	YEAR	CONTEXT
29490021	r	ShinyKGode: an Interactive Application for ODE Parameter Inference Using Gradient Matching.	2018	the [R package] for shiny
29490015	r	Isoform-level gene expression patterns in single-cell RNA-sequencing data.	2018	nted as a [R package] and is av
29490010	python	SECLAF: A Webserver and Deep Neural Network Design Tool for Hierarchical Biological Sequence Classification.	2018	mented in [python], and is a
29486711	r	lme4qtl: linear mixed models with flexible covariance structure for genetic studies of related individuals.	2018	mms). the [R package] lme4 is a
29474733	c	Bacmeta: simulator for genomic evolution in bacterial metapopulations.	2018	simulated [using C] ++ object
29474526	r	IWTomics: testing high-resolution sequence-based Omics data at multiple locations and scales.	2018	le at the [Bioconductor] website (
29462241	r	flowLearn: Fast and precise identification and quality checking of cell populations in flow cytometry.	2018	ble as an [R package] on https:
29458351	r	CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses.	2018	cemitool [R package] provides
29447401	r	RaMWAS: Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms.	2018	conductor [R package] called ra
29444641	java	Oasis 2: improved online analysis of small RNA-seq data.	2018	mented in [java], j2ee, my
29444641	python	Oasis 2: improved online analysis of small RNA-seq data.	2018	e, mysql, [python], r, php a
29444641	javascript	Oasis 2: improved online analysis of small RNA-seq data.	2018	, php and [javascript]. it is fr
29444236	r	findGSE: estimating genome size variation within human and Arabidopsis using k-mer frequencies.	2018	[R package] of findgs
29444234	python	ThreaDNA: predicting DNA mechanics' contribution to sequence selectivity of proteins along whole genomes.	2018	[python] software
29444205	python	ssbio: A Python Framework for Structural Systems Biology.	2018	ssbio: a [python] framework
29438558	r	KMgene: a unified R package for gene-based association analysis for complex traits.	2018	a unified [R package] for gene-
29438498	r	chromswitch: A flexible method to detect chromatin state switches.	2018	ted as an [R package] available
29432517	mathlab	Spectral clustering based on learning similarity matrix.	2018	mented in [matlab]. the sour
29432514	r	Improving SNP Prioritization and Pleiotropic Architecture Estimation by Incorporating Prior Knowledge Using graph-GPA.	2018	ted as an [R package] 'ggpa', w
29420693	r	FWER and FDR Control When Testing Multiple Mediators.	2018	[R package] multimed
29420676	mathlab	Principal Metabolic Flux Mode Analysis.	2018	[matlab] software
29415263	mathlab	scEpath: Energy landscape-based inference of transition probabilities and cellular trajectories from single-cell transcriptomic data.	2018	a [matlab] package o
29401218	javascript	MutHTP: Mutations in Human Transmembrane Proteins.	2018	, php and [javascript] and suppo
29401212	python	GEMMER: GEnome-wide tool for Multi-scale Modeling data Extraction and Representation for Saccharomyces cerevisiae.	2018	ritten in [python], javascri
29401212	javascript	GEMMER: GEnome-wide tool for Multi-scale Modeling data Extraction and Representation for Saccharomyces cerevisiae.	2018	n python, [javascript] library d
29394323	python	pymzML v2.0: introducing a highly compressed and seekable gzip format.	2018	requires [python3].4+ and op
29390967	javascript	Cross-linking BioThings APIs through JSON-LD to facilitate knowledge exploration.	2018	e adopted [javascript] object no
29385404	python	TOXsIgN: a cross-species repository for toxicogenomic signatures.	2018	mented in [python], javascri
29385404	javascript	TOXsIgN: a cross-species repository for toxicogenomic signatures.	2018	n python, [javascript], and mong
29385403	r	TSAPA: identification of tissue-specific alternative polyadenylation sites in plants.	2018	eloped an [R package] called ts
29361904	python	Spherical: an iterative workflow for assembling metagenomic datasets.	2018	mented in [python], to addre
29360996	r	Feature Specific Quantile Normalization Enables Cross-Platform Classification of Molecular Subtypes using Gene Expression Data.	2018	ted as an [R package] to cran.
29360936	python	Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements.	2018	platform, [python] package c
29357822	javascript	MutScan: fast detection and visualization of target mutations by scanning FASTQ data.	2018	html and [javascript]. algorith
29346510	java	VIPER: a web application for rapid expert review of variant calls.	2018	mented in [java] and javas
29346510	javascript	VIPER: a web application for rapid expert review of variant calls.	2018	java and [javascript] and is fr
29346509	r	A distance-based approach for testing the mediation effect of the human microbiome.	2018	an [R package] medtest
29342241	java	iPat: Intelligent Prediction and Association Tool for Genomic Research.	2018	ritten in [java] for adapt
29342236	r	MAGNAMWAR: An R package for genome-wide association studies of bacterial orthologs.	2018	amwar: an [R package] for genom
29342233	r	QuantumClone: Clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction.	2018	ntumclone [R package] are freel
29340616	python	PyChimera: Use UCSF Chimera modules in any Python 2.7 project.	2018	es in any [python] 2.7 proje
29340599	r	A benchmark study of scoring methods for non-coding mutations.	2018	ake, c ++ [and R] codes are
29334888	r	diceR: an R package for class discovery using an ensemble driven approach.	2018	dicer: an [R package] for class
29329398	python	LeNup: Learning Nucleosome positioning from DNA sequences with improved convolutional neural networks.	2018	ilable as [python] and lua s
29329372	r	Enrichment analysis with EpiAnnotator.	2018	tor is an [R package] accompani
29315360	r	CGManalyzer:an R package for analyzing continuous glucose monitoring studies.	2018	alyzer:an [R package] for analy
29310570	r	Thresher: determining the number of clusters while removing outliers.	2018	ted in an [R package] called th
29309511	r	DiffGraph: An R package for identifying gene network rewiring using differential graphical models.	2017	graph: an [R package] for ident
29300846	python	ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data.	2017	ritten in [python] and c ++
29300845	python	ChronQC: A Quality Control Monitoring System for Clinical Next Generation Sequencing.	2017	) and the [python] package i
29297298	mathlab	2D-EM clustering approach for high-dimensional data through folding feature vectors.	2017	methods. [matlab] implement
29297297	mathlab	Divisive hierarchical maximum likelihood clustering.	2017	logies. a [matlab] implement
29297289	javascript	dBBQs: dataBase of Bacterial Quality scores.	2017	teractive [javascript] chart fra
29293946	r	polyPK: An R package for pharmacokinetic analysis of multi-component drugs using a metabolomics approach.	2017	olypk: an [R package] for pharm
29293920	java	Towards Self-Learning Based Hypotheses Generation in Biomedical Text Domain.	2017	relevant [java] codes are
29291710	r	Simulating autosomal genotypes with realistic linkage disequilibrium and a spiked-in genetic effect.	2018	hod in an [R package] (triadsim
29280999	r	Multiple hot-deck imputation for network inference from RNA sequencing data.	2017	ble as an [R package], rnaseqne
29280991	r	R2DGC: Threshold-free peak alignment and identification for 2D gas chromatography mass spectrometry in R.	2017	eloped an [R package] that impl
29272352	r	Missing value imputation for LC-MS metabolomics data by incorporating metabolic network and adduct ion relations.	2017	the [R package] is availa
29267850	r	Rcupcake: an R package for querying and analyzing biomedical data through the BD2K PIC-SURE RESTful API.	2017	pcake: an [R package] for query
29267848	python	ProbAnnoWeb and ProbAnnoPy: probabilistic annotation and gap-filling of metabolic reconstructions.	2017	tandalone [python] package c
29258445	java	A biological network-based regularized artificial neural network model for robust phenotype prediction from gene expression data.	2017	provide a [java] code of o
29253085	python	JASPAR RESTful API: accessing JASPAR data from any programming language.	2017	mented in [python] using the
29253072	r	K2 and K*2: Efficient alignment-free sequence similarity measurement based on Kendall statistics.	2017	ed in the [R language] as a pack
29244013	java	Cache and energy efficient algorithms for Nussinov's RNA Folding.	2017	pose. the [java] versions
29244010	mathlab	RocSampler: regularizing overlapping protein complexes in protein-protein interaction networks.	2017	ampler in [matlab] and its e
29240889	java	GeoBoost: accelerating research involving the geospatial metadata of virus GenBank records.	2017	mented in [java] 1.8, and
29237399	r	Redundancy analysis allows improved detection of methylation changes in large genomic regions.	2017	n meal, a [Bioconductor] package d
29237398	python	pyAmpli: an amplicon-based variant filter pipeline for targeted resequencing data.	2017	allelized [python] package t
29236977	r	gene2drug: a Computational Tool for Pathway-based Rational Drug Repositioning.	2017	em.it. an [R package] is under
29236969	r	DaMiRseq-an R/Bioconductor package for data mining of RNA-Seq data: normalization, feature selection and classification.	2017	rs at the [Bioconductor] open-sour
29236954	python	NGLview - Interactive molecular graphics for Jupyter notebooks.	2017	/nglview. [python] packages
29236954	javascript	NGLview - Interactive molecular graphics for Jupyter notebooks.	2017	-side and [javascript] on the cl
29228294	bash	Accurate Mapping of tRNA Reads.	2017	both as a [bash] script an
29228182	python	PEITH(Θ) - Perfecting Experiments with Information Theory in Python with GPU support.	2017	theory in [python] with gpu
29212440	python	CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences.	2017	onomy), a [python] tool that
29206901	mathlab	GenSSI 2.0: Multi-experiment structural identifiability analysis of SBML models.	2017	range of [matlab] versions
29194472	r	ThetaMater: Bayesian estimation of population size parameter θ from genomic data.	2017	en source [R package] comprisin
29194470	r	iDINGO - Integrative Differential Network Analysis in Genomics with Shiny Application.	2017	he idingo [R package] to estima
29187149	r	DBNorm: normalizing high-density oligonucleotide microarray data based on distributions.	2017	ted as an [R package], is an al
29187143	python	DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data.	2017	ritten in [python] and r, an
29187143	r	DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data.	2017	in python [and R], and is s
29186450	java	SPECTRE: a Suite of PhylogEnetiC Tools for Reticulate Evolution.	2017	ritten in [java], that com
29186355	mathlab	Global proteomics profiling improves drug sensitivity prediction: results from a multi-omics, pan-cancer modeling approach.	2017	s well as [matlab] implement
29186344	perl	MOCASSIN-prot: A Multi-Objective Clustering Approach for Protein Similarity Networks.	2017	mented in [perl] and matla
29186344	mathlab	MOCASSIN-prot: A Multi-Objective Clustering Approach for Protein Similarity Networks.	2017	perl and [matlab], is freel
29186339	java	bioalcidae, samjs and vcffilterjs: object-oriented formatters and filters for bioinformatics files.	2017	or a pure [java] expressio
29186339	javascript	bioalcidae, samjs and vcffilterjs: object-oriented formatters and filters for bioinformatics files.	2017	s using a [javascript] engine or
29186333	python	FUn: A Framework for Interactive Visualizations of Large, High Dimensional Datasets on the Web.	2017	kages and [python] libraries
29186328	r	Meta-analytic Principal Component Analysis in Integrative Omics Application.	2017	an [R package] metapca i
29186322	java	SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles.	2017	ritten in [java] and freel
29186321	java	Mapping-free variant calling using haplotype reconstruction from k-mer frequencies.	2017	ion for a [java] implement
29186298	python	SimulaTE: Simulating complex landscapes of transposable elements of populations.	2017	mented in [python] and avail
29186290	perl	scHiCNorm: A Software Package to Eliminate Systematic Biases in Single-Cell Hi-C Data.	2017	hicnorm/. [perl] scripts a
29186288	java	Reproducible and flexible simulation experiments with ML-Rules and SESSL.	2017	mented in [java], sessl an
29186284	c	CALQ: compression of quality values of aligned sequencing data.	2017	calq is [written in C] ++ and ca
29178844	r	BoolFilter: an R package for estimation and identification of partially-observed Boolean dynamical systems.	2017	ilter: an [R package] for estim
29166858	r	ADAGE signature analysis: differential expression analysis with data-defined gene sets.	2017	d both an [R package] (adagepat
29162056	perl	Synima: a Synteny imaging tool for annotated genome assemblies.	2017	ritten in [perl], which us
29155928	python	Modeling positional effects of regulatory sequences with spline transformations increases prediction accuracy of deep neural networks.	2017	e concise [python] package:
29151019	r	bcROCsurface: an R package for correcting verification bias in estimation of the ROC surface and its volume for continuous diagnostic tests.	2017	rface: an [R package] for corre
29145823	r	dbMDEGA: a database for meta-analysis of differentially expressed genes in autism spectrum disorder.	2017	e applied [R language] software
29132318	c++	BugMat and FindNeighbour: command line and server applications for investigating bacterial relatedness.	2017	is a fast [C++] applicati
29126132	python	Cost-effective and accurate method of measuring fetal fraction using SNP imputation.	2017	[python] source co
29121165	python	PERF: An Exhaustive Algorithm for Ultra-Fast and Efficient Identification of Microsatellites from Large DNA Sequences.	2017	ed in the [python] programmi
29112706	r	NanoStringNormCNV: Pre-processing of NanoString CNV data.	2017	rmcnv, an [R package] for pre-p
29110634	java	JS-MS: a cross-platform, modular javascript viewer for mass spectrometry signals.	2017	a modular [java] backend w
29110634	javascript	JS-MS: a cross-platform, modular javascript viewer for mass spectrometry signals.	2017	, modular [javascript] viewer fo
29106469	python	DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication.	2017	mented in [python] 3 and run
29106443	r	Estimation of QTL heritability based on pooled sequencing data.	2017	uires the [R package] rootsolve
29106441	python	orchid: a novel management, annotation, and machine learning framework for analyzing cancer mutations.	2017	orchid, a [python] based sof
29095980	javascript	pedigreejs: a web-based graphical pedigree editor.	2017	ritten in [javascript], which us
29095974	python	BEAM web server: A tool for structural RNA motif discovery.	2017	odejs and [python] with all
29092015	java	MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota.	2018	ritten in [java] and is pl
29092009	r	Machine learning annotation of human branchpoints.	2017	ogramming [language r] and is fr
29091997	r	Efficient comparative phylogenetics on large trees.	2017	ent a new [R package], named c
29091996	javascript	Visualization portal for genetic variation (VizGVar): a tool for interactive visualization of SNPs and somatic mutations in exons, genes and protein domains.	2017	web-based [javascript] visualiza
29088314	r	An exact test for comparing a fixed quantitative property between gene sets.	2017	ilable on [CRAN].
29088309	python	DIEGO: Detection of Differential Alternative Splicing using Aitchison's Geometry.	2017	the [python] tool dieg
29088309	perl	DIEGO: Detection of Differential Alternative Splicing using Aitchison's Geometry.	2017	ython and [perl] parsers f
29087464	python	MutaNET: a tool for automated analysis of genomic mutations in gene regulatory networks.	2017	mented in [python] and suppo
29087446	r	ndexr-an R package to interface with the network data exchange.	2018	ndexr-an [R package] to interf
29087435	javascript	Dynamic Assessment of Microbial Ecology (DAME): A web app for interactive analysis and visualization of microbial sequencing data.	2017	css, and [javascript]. it is fr
29077810	python	ISEScan: automated identification of insertion sequence elements in prokaryotic genomes.	2017	mented in [python] and relea
29077807	r	pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R.	2017	developed [Bioconductor] package f
29077797	c++	netReg: Network-regularized linear models for biological association studies.	2017	ckage and [C++] commandli
29077797	r	netReg: Network-regularized linear models for biological association studies.	2017	tion. the [R package] is freely
29077795	r	Group Spike-and-Slab Lasso Generalized Linear Models for Disease Prediction and Associated Genes Detection by Incorporating Pathway Information.	2017	available [R package] bhglm (ht
29077792	r	Unsupervised multiple kernel learning for heterogeneous data integration.	2017	le in the [R package] mixkernel
29069317	mathlab	Constructing Prediction Models from Expression Profiles for Large Scale lncRNA-miRNA Interaction Profiling.	2017	[matlab] codes and
29069312	mathlab	PESTO: Parameter EStimation TOolbox.	2018	mathworks [matlab]. it offer
29069305	r	heatmaply: an R package for creating interactive cluster heatmaps for online publishing.	2017	maply: an [R package] for creat
29061110	mathlab	A rapid and accurate approach for prediction of interactomes from co-elution data (PrInCE).	2017	mented in [matlab] (version
29048524	python	Krait: an ultrafast tool for genome-wide survey of microsatellites and primer design.	2018	in c and [python], and supp
29048466	python	PyBEL: a computational framework for Biological Expression Language.	2018	universal [python] code. its
29045591	c	SAGE2: parallel human genome assembly.	2018	sage2 is [written in C] ++ and op
29040453	mathlab	Detection of Sputum by Interpreting the Time-frequency Distribution of Respiratory Sound Signal Using Image Processing Techniques.	2017	the [matlab] codes and
29040451	r	An omnibus test for differential distribution analysis of microbiome sequencing data.	2018	[R package] is availa
29040384	mathlab	SELANSI: a toolbox for Simulation of Stochastic Gene Regulatory Networks.	2017	under the [matlab] environme
29037149	r	chngpt: threshold regression model estimation and inference.	2017	the [R package] chngpt pr
29036584	python	cgHeliParm: analysis of dsDNA helical parameters for coarse-grained MARTINI molecular dynamics simulations.	2017	liparm, a [python] program t
29036584	r	cgHeliParm: analysis of dsDNA helical parameters for coarse-grained MARTINI molecular dynamics simulations.	2017	examples [and R] scripts a
29036562	r	nandb-number and brightness in R with a novel automatic detrending algorithm.	2017	an [R package] for perfo
29036558	python	MethRaFo: MeDIP-seq methylation estimate using a Random Forest Regressor.	2017	able as a [python] package (
29036557	python	Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models.	2017	altab and [python] scripts a
29036546	java	CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing.	2017	mented in [java]. crocobla
29036536	python	wft4galaxy: a workflow testing tool for galaxy.	2017	a regular [python] program o
29036513	r	ScanGEO: parallel mining of high-throughput gene expression data.	2017	e code is [written in R] and imple
29036507	r	ggseqlogo: a versatile R package for drawing sequence logos.	2017	versatile [R package] for drawi
29036452	python	A nonparametric significance test for sampled networks.	2018	ritten in [python] and uses
29036400	r	Prediction and modeling of pre-analytical sampling errors as a strategy to improve plasma NMR metabolomics data.	2017	mpledrift [R package] is availa
29036359	r	proFIA: a data preprocessing workflow for flow injection analysis coupled to high-resolution mass spectrometry.	2017	ble as an [R package] on the bi
29036320	r	Detect differentially methylated regions using non-homogeneous hidden Markov model for methylation array data.	2017	ble as an [R package] at the cr
29036318	r	DIMM-SC: a Dirichlet mixture model for clustering droplet-based single cell transcriptomic data.	2018	-friendly [R package] with a de
29036307	mathlab	Irys Extract.	2018	eloped in [matlab] r2015a, i
29036291	python	Phylotyper: in silico predictor of gene subtypes.	2017	yper is a [python] and r pac
29036291	r	Phylotyper: in silico predictor of gene subtypes.	2017	ython and [R package]. it is av
29036287	r	powsimR: power analysis for bulk and single cell RNA-seq experiments.	2017	the [R package] and assoc
29036277	python	PySeqLab: an open source Python package for sequence labeling and segmentation.	2017	en source [python] package f
29029016	r	diffuStats: an R package to compute diffusion-based scores on biological networks.	2018	stats: an [R package] to comput
29028963	r	ZCCHC17 is a master regulator of synaptic gene expression in Alzheimer's disease.	2018	matlab [and R] scripts u
29028963	mathlab	ZCCHC17 is a master regulator of synaptic gene expression in Alzheimer's disease.	2018	[matlab] and r scr
29028961	r	Towards unified quality verification of synthetic count data with countsimQC.	2018	ted as an [R package] (for r ve
29028923	r	Detecting presence of mutational signatures in cancer with confidence.	2017	ted in an [R package], called s
29028911	r	Genome-wide pre-miRNA discovery from few labeled examples.	2018	an [R package] can be do
29028902	python	graphkernels: R and Python packages for graph comparison.	2018	ls: r and [python] packages
29028896	python	PyDREAM: high-dimensional parameter inference for biological models in python.	2018	models in [python].
29028890	r	MALDIrppa: quality control and robust analysis for mass spectrometry data.	2018	this [R package] helps to
29028267	r	VariantTools: an extensible framework for developing and testing variant callers.	2017	ttp://www.[Bioconductor].org/.
29028264	javascript	TeachEnG: a Teaching Engine for Genomics.	2017	ritten in [javascript] and compa
29028262	r	TSIS: an R package to infer alternative splicing isoform switches for time-series data.	2017	tsis: an [R package] to infer
29028260	r	pulseR: Versatile computational analysis of RNA turnover from metabolic labeling experiments.	2017	he pulser [R package] simplifie
29025394	r	Prediction of Human Phenotype Ontology terms by means of hierarchical ensemble methods.	2017	ble as an [R package] from the
29017446	python	LSTrAP: efficiently combining RNA sequencing data into co-expression networks.	2017	mented in [python] 3.4 (or h
28981576	r	SEGtool: a specifically expressed gene detection tool and applications in human tissue and single-cell sequencing data.	2017	f segtool [R package] is freely
28981573	r	OPATs: Omnibus P-value association tests.	2017	mmed in r [and R] graphical
28974199	r	Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data.	2017	an [R package] instantia
28968872	python	PySCeSToolbox: a collection of metabolic pathway analysis tools.	2018	on to the [python] simulator
28968815	mathlab	A Novel SCCA Approach via Truncated ℓ1-norm and Truncated Group Lasso for Brain Imaging Genetics.	2017	the [matlab] code and
28968783	java	SMLocalizer, a GPU accelerated ImageJ plugin for single molecule localization microscopy.	2018	n imagej. [java] and cuda
28968706	r	LinkageMapView - Rendering High Resolution Linkage and QTL Maps.	2017	n package [written in R] that prod
28968704	r	SINCERITIES: Inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles.	2017	he matlab [and R] version o
28968704	mathlab	SINCERITIES: Inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles.	2017	the [matlab] and r ver
28968701	python	Interactive network visualization in Jupyter notebooks: visJS2jupyter.	2018	ps://pypi.[python].org/pypi/
28968701	javascript	Interactive network visualization in Jupyter notebooks: visJS2jupyter.	2018	uses the [javascript] library v
28968690	r	regNet: An R package for network-based propagation of gene expression alterations.	2017	egnet: an [R package] for netwo
28968682	r	Identification and visualization of differential isoform expression in RNA-seq time series.	2018	ty of the [R package] masigpro
28968671	r	Three-dimensional cardiovascular imaging-genetics: a mass univariate framework.	2018	ded in an [R package] freely av
28968667	mathlab	Genome-scale fluxes predicted under the guidance of enzyme abundance using a novel hyper-cube shrink algorithm.	2018	mented by [matlab] and c ++.
28968663	mathlab	Morphologically constrained and data informed cell segmentation of budding yeast.	2018	the [matlab] code for
28968645	python	Kfits: a software framework for fitting and cleaning outliers in kinetic measurements.	2018	mented in [python] and avail
28968644	r	Phosphonormalizer: an R package for normalization of MS-based label-free phosphoproteomics.	2018	lizer: an [R package] for norma
28968630	r	Pathway enrichment analysis approach based on topological structure and updated annotation of pathway.	2017	eloped an [R package] to implem
28962546	c++	pulver: an R package for parallel ultra-rapid p-value computation for linear regression interaction terms.	2017	language [C++]. furtherm
28962546	r	pulver: an R package for parallel ultra-rapid p-value computation for linear regression interaction terms.	2017	ulver: an [R package] for paral
28961999	r	Prediction of delayed retention of antibodies in hydrophobic interaction chromatography from sequence using machine learning.	2017	st-cases, [and R] scripts u
28961965	java	Real-time demultiplexing Nanopore barcoded sequencing data with npBarcode.	2017	n japsa-a [java] tools kit
28961912	r	Enabling reproducible real-time quantitative PCR research: the RDML package.	2017	computing [language r]. rdml is
28961895	mathlab	HiDi: an efficient reverse engineering schema for large-scale dynamic regulatory network reconstruction using adaptive differentiation.	2017	the [matlab] code of t
28961861	r	Conditional asymptotic inference for the kernel association test.	2017	ed in the [R package] igasso.
28961782	c	MetaCache: context-aware classification of metagenomic reads using minhashing.	2017	software [written in C] ++ and ca
28961763	r	psygenet2r: a R/Bioconductor package for the analysis of psychiatric disease genes.	2017	net2r, an [R package] that cont
28961761	r	clustComp, a bioconductor package for the comparison of clustering results.	2017	stcomp, a [Bioconductor] package f
28961756	mathlab	4D nucleome Analysis Toolbox: analysis of Hi-C data with abnormal karyotype and time series capabilities.	2018	powerful [matlab] toolbox f
28961747	r	An improved compound Poisson model for the number of motif hits in DNA sequences.	2017	able as a [Bioconductor] package n
28961746	r	ChAMP: updated methylation analysis pipeline for Illumina BeadChips.	2017	on of the [Bioconductor] package c
28961742	perl	BSviewer: a genotype-preserving, nucleotide-level visualizer for bisulfite sequencing data.	2017	mented in [perl] and runs
28961740	python	EMHP: an accurate automated hole masking algorithm for single-particle cryo-EM image processing.	2017	s minimal [python] dependenc
28961706	r	Genome-wide association studies using a penalized moving-window regression.	2017	ovided in [R package] mwlasso.
28961702	r	MWASTools: an R/Bioconductor package for metabolome-wide association studies.	2017	ols is an [R package] designed
28957498	r	ClusterSignificance: a bioconductor package facilitating statistical analysis of class cluster separations in dimensionality reduced data.	2017	nce is an [R package] available
28927242	r	biospear: an R package for biomarker selection in penalized Cox regression.	2018	spear: an [R package] for bioma
28923005	r	Methods for discovering genomic loci exhibiting complex patterns of differential methylation.	2017	egmentseq [R package] is extend
28911038	perl	Spliceman2: a computational web server that predicts defects in pre-mRNA splicing.	2017	ache, and [perl], with all
28882003	python	miniMDS: 3D structural inference from high-resolution Hi-C data.	2017	a [python] implement
28881993	java	Genomes as documents of evolutionary history: a probabilistic macrosynteny model for the reconstruction of ancestral genomes.	2017	ritten in [java] is availa
28881990	r	A new method to study the change of miRNA-mRNA interactions due to environmental exposures.	2017	[R package] ijrf is a
28881987	mathlab	Efficient simulation of intrinsic, extrinsic and external noise in biochemical systems.	2017	nsight, a [matlab] script is
28881985	mathlab	popFBA: tackling intratumour heterogeneity with Flux Balance Analysis.	2017	he popfba [matlab] function
28881984	mathlab	Estimation of time-varying growth, uptake and excretion rates from dynamic metabolomics data.	2017	the [matlab] code for
28881983	mathlab	A scalable moment-closure approximation for large-scale biochemical reaction networks.	2017	en-source [matlab] toolbox c
28881979	mathlab	Identification of associations between genotypes and longitudinal phenotypes via temporally-constrained group sparse canonical correlation analysis.	2017	the [matlab] code is a
28881975	r	Molecular signatures that can be transferred across different omics platforms.	2017	lete data [and R] codes nec
28881967	mathlab	HopLand: single-cell pseudotime recovery using continuous Hopfield network-based modeling of Waddington's epigenetic landscape.	2017	the [matlab] implement
28750623	r	l1kdeconv: an R package for peak calling analysis with LINCS L1000 data.	2017	econv: an [R package] for peak
28724417	r	Examining the role of unmeasured confounding in mediation analysis with genetic and genomic applications.	2017	mediation [R package] enables t
28716000	python	Quantiprot - a Python package for quantitative analysis of protein sequences.	2017	iprot - a [python] package f
28683752	r	TnseqDiff: identification of conditionally essential genes in transposon sequencing studies.	2017	nction in [R package] tnseq and
28676075	r	sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters.	2017	gnesr: an [R package] for simul
28673016	mathlab	FALCON: a toolbox for the fast contextualization of logical networks.	2017	propose a [matlab] toolbox,
28666369	r	CausalR: extracting mechanistic sense from genome scale data.	2017	able from [Bioconductor].
28666322	python	SVM-dependent pairwise HMM: an application to protein pairwise alignments.	2017	a [python] implement
28666320	mathlab	Inferring transcriptional logic from multiple dynamic experiments.	2017	ritten in [matlab] and stati
28666314	python	GPU-powered model analysis with PySB/cupSODA.	2017	from the [python] package i
28659129	python	SLMSuite: a suite of algorithms for segmenting genomic profiles.	2017	e them in [python], ruby and
28659129	c++	SLMSuite: a suite of algorithms for segmenting genomic profiles.	2017	ruby and [C++]. slmsuite
28655158	python	CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes.	2017	ritten in [python] and avail
28655153	r	The KSEA App: a web-based tool for kinase activity inference from quantitative phosphoproteomics.	2017	le as the [R package] kseaapp
28651569	mathlab	ReTrOS: a MATLAB toolbox for reconstructing transcriptional activity from gene and protein expression data.	2017	retros: a [matlab] toolbox f
28651334	r	TSGSIS: a high-dimensional grouped variable selection approach for detection of whole-genome SNP-SNP interactions.	2017	d through [CRAN] and is av
28651329	java	High-speed and high-ratio referential genome compression.	2017	c ++ and [java] source co
28645171	r	UpSetR: an R package for the visualization of intersecting sets and their properties.	2017	psetr: an [R package] for the v
28645150	python	GfaPy: a flexible and extensible software library for handling sequence graphs in Python.	2017	graphs in [python].
28637232	python	PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies.	2017	ritten in [python3] and r und
28637232	r	PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies.	2017	n python3 [and R] under the
28637183	python	NucliTrack: an integrated nuclei tracking application.	2017	en source [python] package.
28637183	mathlab	NucliTrack: an integrated nuclei tracking application.	2017	itrack. a [matlab] toolbox i
28633423	r	rqt: an R package for gene-level meta-analysis.	2017	rqt: an [R package] for gene-
28633418	r	Detecting and removing multiplicative spatial bias in high-throughput screening technologies.	2017	ilable on [CRAN].
28633357	r	matter: an R package for rapid prototyping with larger-than-memory datasets on disk.	2017	atter: an [R package] for rapid
28633344	java	Pheno4J: a gene to phenotype graph database.	2017	data. our [java] based sol
28633344	python	Pheno4J: a gene to phenotype graph database.	2017	java and [python] code are
28617225	c++	A greedy alignment-free distance estimator for phylogenetic inference.	2017	mented in [C++] and has b
28605539	python	runBNG: a software package for BioNano genomic analysis on the command line.	2017	perl and [python] software.
28605539	bash	runBNG: a software package for BioNano genomic analysis on the command line.	2017	ritten in [bash], with the
28605539	perl	runBNG: a software package for BioNano genomic analysis on the command line.	2017	ges, gcc, [perl] and pytho
28605519	r	CancerSubtypes: an R/Bioconductor package for molecular cancer subtype identification, validation and visualization.	2017	types, an [R package] for ident
28605449	python	FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool.	2017	mented in [python] 3 and jav
28605449	javascript	FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool.	2017	hon 3 and [javascript], and is m
28595310	r	Phantom: investigating heterogeneous gene sets in time-course data.	2017	phantom . [R package] of phanto
28587596	r	A systematic evaluation of nucleotide properties for CRISPR sgRNA design.	2017	iency. an [R package] predictsg
28582565	python	ISAMBARD: an open-source computational environment for biomolecular analysis, modelling and design.	2017	from the [python] package i
28582538	python	BreakPoint Surveyor: a pipeline for structural variant visualization.	2017	ted in r, [python] and bash
28582538	bash	BreakPoint Surveyor: a pipeline for structural variant visualization.	2017	ython and [bash] scripts,
28582485	python	COMPASS: the COMPletely Arbitrary Sequence Simulator.	2017	mented in [python] 2.7, and
28582481	python	FunGAP: Fungal Genome Annotation Pipeline using evidence-based gene model evaluation.	2017	ritten in [python] script an
28575207	python	Moran's I quantifies spatio-temporal pattern formation in neural imaging data.	2017	[python] 2.7 code
28575171	r	karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data.	2017	e through [Bioconductor] (http://w
28575169	python	MD-TASK: a software suite for analyzing molecular dynamics trajectories.	2017	mented in [python] and suppo
28558647	c++	Hapl-o-Mat: open-source software for HLA haplotype frequency estimation from ambiguous and heterogeneous data.	2017	mented in [C++], hapl-o-m
28549446	java	gnparser : a powerful parser for scientific names based on Parsing Expression Grammar.	2017	. it is a [java] tool writ
28545397	java	JED: a Java Essential Dynamics Program for comparative analysis of protein trajectories.	2017	jed: a [java] essential
28545397	r	JED: a Java Essential Dynamics Program for comparative analysis of protein trajectories.	2017	sion of q [and R], and repo
28535748	r	DTWscore: differential expression and cell clustering analysis for time-series single-cell RNA-seq data.	2017	datasets [and R] packages
28535188	r	Molecular heterogeneity at the network level: high-dimensional testing, clustering and a TCGA case study.	2017	as the [Bioconductor] package n
28532394	python	CircularLogo: A lightweight web application to visualize intra-motif dependencies.	2017	cript and [python] based on
28532394	javascript	CircularLogo: A lightweight web application to visualize intra-motif dependencies.	2017	mented in [javascript] and pytho
28525538	r	chimeraviz: a tool for visualizing chimeric RNA.	2017	viz is an [R package] available
28525531	javascript	PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization.	2017	using the [javascript] library d
28521770	python	Coordinates and intervals in graph-based reference genomes.	2017	ve made a [python] package f
28520900	mathlab	Accelerating high-dimensional clustering with lossless data reduction.	2017	r, [matlab] and sas/i
28520848	mathlab	Pattern fusion analysis by adaptive alignment of multiple heterogeneous omics data.	2017	nted as a [matlab] package,
28505270	r	HTSvis: a web app for exploratory data analysis and visualization of arrayed high-throughput screens.	2017	en-source [R package], download
28505251	r	False discovery rate control incorporating phylogenetic tree increases detection power in microbiome-wide multiple testing.	2017	[R package] structfdr
28505247	r	Single-cell regulome data analysis by SCRAT.	2017	rat as an [R package].
28505226	java	OMTools: a software package for visualizing and processing optical mapping data.	2017	mented in [java] 1.8 and r
28499413	mathlab	Ranking metrics in gene set enrichment analysis: do they matter?	2017	mented in [matlab], and is a
28498885	python	PROXiMATE: a database of mutant protein-protein complex thermodynamics and kinetics.	2017	mented in [python], and supp
28494801	mathlab	Spectral imaging toolbox: segmentation, hyperstack reconstruction, and batch processing of spectral images for the determination of cell and model membrane lipid order.	2017	present a [matlab] spectral
28481978	r	Application of the cghRA framework to the genomic characterization of Diffuse Large B-Cell Lymphoma.	2017	[R package] and sourc
28481966	r	RankProd 2.0: a refactored bioconductor package for detecting differentially expressed features in molecular profiling datasets.	2017	efactored [Bioconductor] package f
28475668	java	MarDRe: efficient MapReduce-based removal of duplicate DNA reads in the cloud.	2017	ritten in [java] to maximi
28475666	r	Assembling draft genomes using contiBAIT.	2017	ilable on [Bioconductor]. source f
28475662	r	twoddpcr: an R/Bioconductor package and Shiny app for Droplet Digital PCR analysis.	2017	en source [R package] 'twoddpcr
28472919	javascript	WebGIVI: a web-based gene enrichment analysis and visualization tool.	2017	document [javascript] libraries
28472395	mathlab	SinCHet: a MATLAB toolbox for single cell heterogeneity analysis in cancer.	2017	inchet: a [matlab] toolbox f
28472345	python	STOPGAP: a database for systematic target opportunity assessment by genetic association predictions.	2017	perl and [python] scripts a
28472345	perl	STOPGAP: a database for systematic target opportunity assessment by genetic association predictions.	2017	shell, r, [perl] and pytho
28472273	r	EBT: a statistic test identifying moderate size of significant features with balanced power and precision for genome-wide rate comparisons.	2017	an [R package] implement
28472272	python	modlAMP: Python for antimicrobial peptides.	2017	modlamp: [python] for antim
28472271	r	Annotating function to differentially expressed LincRNAs in myelodysplastic syndrome using a network-based method.	2017	mented in [R language] and matla
28472271	mathlab	Annotating function to differentially expressed LincRNAs in myelodysplastic syndrome using a network-based method.	2017	guage and [matlab].
28472248	r	Accounting for tumor purity improves cancer subtype classification from DNA methylation data.	2017	s part of [R package] infiniump
28472230	python	OMSim: a simulator for optical map data.	2017	the [python] simulatio
28472220	r	The spike-and-slab lasso Cox model for survival prediction and associated genes detection.	2017	available [R package] bhglm ( h
28464826	java	microTaboo: a general and practical solution to the k-disjoint problem.	2017	, running [java] 7 and hig
28464823	r	Zipper plot: visualizing transcriptional activity of genomic regions.	2017	ogramming [language r] and is fr
28453684	python	MAPPI-DAT: data management and analysis for protein-protein interaction data from the high-throughput MAPPIT cell microarray platform.	2017	eloped in [python], using r
28453684	r	MAPPI-DAT: data management and analysis for protein-protein interaction data from the high-throughput MAPPIT cell microarray platform.	2017	n python, [using R] for data
28453675	javascript	CircosVCF: circos visualization of whole-genome sequence variations stored in VCF files.	2017	mented in [javascript] and is av
28453674	c	ntCard: a streaming algorithm for cardinality estimation in genomics data.	2017	ntcard is [written in C] ++ and is
28453672	python	Primerize-2D: automated primer design for RNA multidimensional chemical mapping.	2017	and-alone [python] package f
28453670	r	GppFst: genomic posterior predictive simulations of FST and dXY for identifying outlier loci from population genomic data.	2017	en source [R package] that gene
28453611	r	modSaRa: a computationally efficient R package for CNV identification.	2017	efficient [R package] for cnv i
28449031	python	RNAblueprint: flexible multiple target nucleic acid sequence design.	2017	ritten in [python] to demons
28444139	mathlab	Multi-label classifier based on histogram of gradients for predicting the anatomical therapeutic chemical class/classes of a given compound.	2017	the [matlab] code for
28444126	r	CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets.	2017	uses the [R package] drc for a
28431087	mathlab	A method for learning a sparse classifier in the presence of missing data for high-dimensional biological datasets.	2017	a [matlab] implement
28430977	java	Deep mining heterogeneous networks of biomedical linked data to predict novel drug-target associations.	2017	eloped in [java] and it is
28420344	python	Erratum to: The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism.	2017	(jqmm): a [python] library f
28419235	r	A Bayesian group sparse multi-task regression model for imaging genetics.	2017	ble as an [R package] 'bgsmtr'
28410574	r	Comparison of different cell type correction methods for genome-scale epigenetics studies.	2017	the minfi [R package], the meth
28407035	javascript	IcyTree: rapid browser-based visualization for phylogenetic trees and networks.	2017	ient-side [javascript] (no plugi
28407034	r	Network module-based model in the differential expression analysis for RNA-seq.	2017	the [R package] seqmade i
28402395	python	mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data.	2017	a set of [python] packages
28402393	r	MetCirc: navigating mass spectral similarity in high-resolution MS/MS metabolomics data.	2017	en-source [R language], together
28398543	r	FunChIP: an R/Bioconductor package for functional classification of ChIP-seq shapes.	2017	from the [Bioconductor] website (
28398503	r	Systemic evaluation of cellular reprogramming processes exploiting a novel R-tool: eegc.	2017	eegc [R package] is releas
28398502	python	PyGOLD: a python based API for docking based virtual screening workflow generation.	2017	pygold: a [python] based api
28398468	r	RTK: efficient rarefaction analysis of large datasets.	2017	c ++ [and R] source co
28398456	java	GARN2: coarse-grained prediction of 3D structure of large RNA molecules by regret minimization.	2017	ritten in [java]. it is fr
28388874	python	Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data.	2017	ompatible [python] package a
28383704	python	ploidyNGS: visually exploring ploidy with Next Generation Sequencing data.	2017	mented in [python] and r.
28383704	r	ploidyNGS: visually exploring ploidy with Next Generation Sequencing data.	2017	in python [and R].
28381205	python	The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism.	2017	(jqmm): a [python] library f
28379466	python	Mackinac: a bridge between ModelSEED and COBRApy to generate and analyze genome-scale metabolic models.	2017	ckinac, a [python] package t
28379351	java	SQC: secure quality control for meta-analysis of genome-wide association studies.	2017	mented in [java] and is pu
28379302	r	cnAnalysis450k: an R package for comparative analysis of 450k/EPIC Illumina methylation array derived copy number data.	2017	s450k: an [R package] for compa
28369371	perl	EUPAN enables pan-genome studies of a large number of eukaryotic genomes.	2017	mented in [perl], r and c
28369339	python	HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps.	2017	julia and [python], and deta
28369316	r	annotatr: genomic regions in context.	2017	annotatr [Bioconductor] package t
28369284	python	Spresso: an ultrafast compound pre-screening method based on compound decomposition.	2017	c ++ and [python], and is a
28369284	c	Spresso: an ultrafast compound pre-screening method based on compound decomposition.	2017	presso is [written in C] ++ and py
28369277	r	GenoGAM: genome-wide generalized additive models for ChIP-Seq analysis.	2017	tps://www.[Bioconductor].org/packa
28369256	mathlab	Entropy-based consensus clustering for patient stratification.	2017	the [matlab] package i
28369250	r	rMSI: an R package for MS imaging data handling and visualization.	2017	rmsi: an [R package] for ms im
28369225	java	Aozan: an automated post-sequencing data-processing pipeline.	2017	mented in [java] and pytho
28369225	python	Aozan: an automated post-sequencing data-processing pipeline.	2017	java and [python], supporte
28369222	r	EthSEQ: ethnicity annotation from whole exome sequencing data.	2017	[R package] available
28369214	java	Constructing linkage maps in the genomics era with MapDisto 2.0.	2017	on of new [java] modules t
28369193	mathlab	Sequential computation of elementary modes and minimal cut sets in genome-scale metabolic networks using alternate integer linear programming.	2017	mented in [matlab], and is p
28369168	python	ConKit: a python interface to contact predictions.	2017	conkit: a [python] interface
28369166	python	Cpipe: a comprehensive computational platform for sequence and structure-based analyses of Cysteine residues.	2017	mented in [python] and freel
28361684	r	NEArender: an R package for functional interpretation of 'omics' data via network enrichment analysis.	2017	ender: an [R package] for funct
28361683	mathlab	Comparative network stratification analysis for identifying functional interpretable network biomarkers.	2017	nted as a [matlab] package,
28340552	python	StrAuto: automation and parallelization of STRUCTURE analysis.	2017	e popular [python] program s
28334409	r	SIApopr: a computational method to simulate evolutionary branching trees for analysis of tumor clonal evolution.	2017	ns) is an [R package] to simula
28334395	r	poRe GUIs for parallel and real-time processing of MinION sequence data.	2017	s for the [R package] pore that
28334390	r	SeqArray-a storage-efficient high-performance data format for WGS variant calls.	2017	ttp://www.[Bioconductor].org/packa
28334360	python	HLA-MA: simple yet powerful matching of samples using HLA typing results.	2017	mented in [python] 3 and fre
28334349	r	DeepBlueR: large-scale epigenomic analysis in R.	2017	is in the [Bioconductor] ecosystem
28334344	r	Estimating gene regulatory networks with pandaR.	2017	conductor [R package] and is av
28334340	r	Meta-analytic framework for liquid association.	2017	a metala [R package], data and
28334306	java	PeptideMapper: efficient and versatile amino acid sequence and tag mapping.	2017	en source [java] compomics
28334266	python	Phenopolis: an open platform for harmonization and analysis of genetic and phenotypic data.	2017	ted using [python], mongodb,
28334266	bash	Phenopolis: an open platform for harmonization and analysis of genetic and phenotypic data.	2017	d various [bash] shell scr
28334231	javascript	ProtVista: visualization of protein sequence annotations.	2017	ista is a [javascript] component
28334222	r	QRank: a novel quantile regression tool for eQTL discovery.	2017	an [R package] is availa
28334215	mathlab	Systematic inference of functional phosphorylation events in yeast metabolism.	2017	[matlab] codes for
28334199	mathlab	Stepwise inference of likely dynamic flux distributions from metabolic time series data.	2017	mented in [matlab] (version
28334194	python	swga: a primer design toolkit for selective whole genome amplification.	2017	mented in [python] and c and
28334167	r	Identification of genetic outliers due to sub-structure and cryptic relationships.	2017	le in the [R package] stego fro
28334165	r	ctsGE-clustering subgroups of expression data.	2017	rt of the [Bioconductor] project a
28334101	mathlab	RefBool: a reference-based algorithm for discretizing gene expression data.	2017	ilable as [matlab] files in
28334094	r	FUNNEL-GSEA: FUNctioNal ELastic-net regression in time-course gene set enrichment analysis.	2017	mented in [R package] funnel, f
28327092	r	metaX: a flexible and comprehensive software for processing metabolomics data.	2017	eloped an [R package], metax, t
28302053	python	A fast and efficient python library for interfacing with the Biological Magnetic Resonance Data Bank.	2017	efficient [python] library f
28302053	javascript	A fast and efficient python library for interfacing with the Biological Magnetic Resonance Data Bank.	2017	quivalent [javascript] object no
28302051	c++	microclass: an R-package for 16S taxonomy classification.	2017	mented in [C++] but opera
28302051	r	microclass: an R-package for 16S taxonomy classification.	2017	resent an [R package] with tool
28284194	java	ClonoCalc and ClonoPlot: immune repertoire analysis from raw files to publication figures with graphical user interface.	2017	opment in [java] and r is
28284194	r	ClonoCalc and ClonoPlot: immune repertoire analysis from raw files to publication figures with graphical user interface.	2017	wraps the [R package] tcr and f
28264647	r	The Repertoire Dissimilarity Index as a method to compare lymphocyte receptor repertoires.	2017	ted as an [R package], and is a
28259147	r	ProteoModlR for functional proteomic analysis.	2017	and-alone [R package].
28259142	r	Avoiding the pitfalls of gene set enrichment analysis with SetRank.	2017	ble as an [R package] and throu
28253840	r	Model based heritability scores for high-throughput sequencing data.	2017	ed in the [R package] heritseq.
28253836	r	flippant-An R package for the automated analysis of fluorescence-based scramblase assays.	2017	ippant-an [R package] for the a
28241739	r	MINT: a multivariate integrative method to identify reproducible molecular signatures across independent experiments and platforms.	2017	ixomics r [CRAN] package,
28241736	r	BBCAnalyzer: a visual approach to facilitate variant calling.	2017	call. the [R package] is freely
28231764	r	stpm: an R package for stochastic process model.	2017	stpm: an [R package] for stoch
28231760	c++	Meta-aligner: long-read alignment based on genome statistics.	2017	mented in [C++] and runs
28209127	r	repo: an R package for data-centered management of bioinformatic pipelines.	2017	repo: an [R package] for data-
28205676	c	GARLIC: Genomic Autozygosity Regions Likelihood-based Inference and Classification.	2017	garlic is [written in C] ++. sourc
28203714	r	Glimma: interactive graphics for gene expression analysis.	2017	he glimma [R package] is availa
28203707	r	Correlated mutations select misfolded from properly folded proteins.	2017	he decoys ['R'] us databa
28203700	r	Threshold-seq: a tool for determining the threshold in short RNA-seq datasets.	2017	ble as an [R package] at: http:
28200075	r	An approach to infer putative disease-specific mechanisms using neighboring gene networks.	2017	able an a [Bioconductor] package.
28200073	mathlab	AptRank: an adaptive PageRank model for protein function prediction on bi-relational graphs.	2017	the [matlab] code is a
28200033	r	Genome-wide genetic heterogeneity discovery with categorical covariates.	2017	an [R package] fastcmh i
28187713	mathlab	Novel methods to optimize gene and statistic test for evaluation - an application for Escherichia coli.	2017	ram using [matlab] r2014a un
28186257	r	sfinx: an R package for the elimination of false positives from affinity purification-mass spectrometry datasets.	2017	sfinx: an [R package] for the e
28186227	r	OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations.	2017	able from [Bioconductor] for linux
28186226	python	Binning_refiner: improving genome bins through the combination of different binning programs.	2017	mented in [python3] and is fr
28186225	r	VALORATE: fast and accurate log-rank test in balanced and unbalanced comparisons of survival curves and cancer genomics.	2017	this, an [R package] (valorate
28186221	bash	Kollector: transcript-informed, targeted de novo assembly of gene loci.	2017	nted as a [bash] script, a
28185580	python	On the consistency of orthology relationships.	2016	mented in [python] and is av
28185573	python	RGmatch: matching genomic regions to proximal genes in omics data integration.	2016	sy-to-use [python] tool that
28185568	r	Identification of expression patterns in the progression of disease stages by integration of transcriptomic data.	2016	re script [written in R], named ge
28185544	python	PWHATSHAP: efficient haplotyping for future generation sequencing.	2016	eloped in [python] and suppo
28177067	python	GLINT: a user-friendly toolset for the analysis of high-throughput DNA-methylation array data.	2017	requires [python] 2.7 and s
28177064	perl	CPSS 2.0: a computational platform update for the analysis of small RNA sequencing data.	2017	in php + [perl] + r and c
28174903	c	Phyx: phylogenetic tools for unix.	2017	programs [written in C] ++ to exp
28174896	r	PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF.	2017	he cogaps [Bioconductor] package (
28174895	r	cooccurNet: an R package for co-occurrence network construction and analysis.	2017	urnet: an [R package] for co-oc
28172632	r	SEQualyzer: interactive tool for quality control and exploratory analysis of high-throughput RNA structural profiling data.	2017	alyzer is [written in R], is platf
28172529	python	Assocplots: a Python package for static and interactive visualization of multiple-group GWAS results.	2017	cplots: a [python] package f
28172469	r	QUBIC: a bioconductor package for qualitative biclustering analysis of gene co-expression data.	2017	qubic: a [Bioconductor] package f
28172448	java	OMBlast: alignment tool for optical mapping using a seed-and-extend approach.	2017	ented for [java] 1.7 and i
28172447	r	Powerful differential expression analysis incorporating network topology for next-generation sequencing data.	2017	ted in an [R package] pathdeseq
28172414	r	simPATHy: a new method for simulating data from perturbed biological PATHways.	2017	thy is an [R package], it is op
28166716	python	PyHLA: tests for the association between HLA alleles and diseases.	2017	veloped a [python] package c
28165116	r	pETM: a penalized Exponential Tilt Model for analysis of correlated high-dimensional DNA methylation data.	2017	the [R package] 'petm' is
28165111	python	MotifNet: a web-server for network motif analysis.	2017	mented in [python] with data
28165109	python	cyvcf2: fast, flexible variant analysis with Python.	2017	ysis with [python].
28158604	python	Pathway Inspector: a pathway based web application for RNAseq analysis of model and non-model organisms.	2017	eloped in [python], making u
28158442	python	Automated cell type discovery and classification through knowledge transfer.	2017	a [python] package (
28158396	r	FIT: statistical modeling tool for transcriptome dynamics under fluctuating field conditions.	2017	d fit, an [R package] that offe
28158333	r	admixturegraph: an R package for admixture graph manipulation and fitting.	2017	graph: an [R package] for admix
28152980	r	DMDtoolkit: a tool for visualizing the mutated dystrophin protein and predicting the clinical severity in DMD.	2017	d in perl [and R] under the
28152980	perl	DMDtoolkit: a tool for visualizing the mutated dystrophin protein and predicting the clinical severity in DMD.	2017	mented in [perl] and r und
28130242	r	Hierarchical sets: analyzing pangenome structure through scalable set visualizations.	2017	hicalsets [R package] available
28130241	r	Classification of RNA structure change by 'gazing' at experimental data.	2017	asssnitch [R package] is freely
28130233	python	A comprehensive quality control workflow for paired tumor-normal NGS experiments.	2017	requires [python] 2.7 and m
28130232	r	ANAQUIN: a software toolkit for the analysis of spike-in controls for next generation sequencing.	2017	tware and [R package] from bioc
28130227	java	Unrealistic phylogenetic trees may improve phylogenetic footprinting.	2017	mented in [java] and can b
28119308	r	QCEWAS: automated quality control of results of epigenome-wide association studies.	2017	he qcewas [R package]. qcewas e
28119307	java	ASCIIGenome: a command line genome browser for console terminals.	2017	ritten in [java]. conseque
28118818	r	GSAR: Bioconductor package for Gene Set analysis in R.	2017	gsar: [Bioconductor] package f
28114896	java	Processing tracking in jMRUI software for magnetic resonance spectra quantitation reproducibility assurance.	2017	eloped in [java], authors
28110292	r	Biomartr: genomic data retrieval with R.	2017	en source [R package], biomartr
28108449	mathlab	Quantification of fibrous spatial point patterns from single-molecule localization microscopy (SMLM) data.	2017	mented in [matlab].
28105912	python	DGW: an exploratory data analysis tool for clustering and visualisation of epigenomic marks.	2016	en source [python] package.
28096085	perl	Improved orthology inference with Hieranoid 2.	2017	[perl] code free
28096075	r	hppRNA-a Snakemake-based handy parameter-free pipeline for RNA-Seq analysis of numerous samples.	2017	dual perl [and R] scripts,
28096075	perl	hppRNA-a Snakemake-based handy parameter-free pipeline for RNA-Seq analysis of numerous samples.	2017	ndividual [perl] and r scr
28095799	r	MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration.	2017	taset: an [R package] for encap
28093409	python	DeuteRater: a tool for quantifying peptide isotope precision and kinetic proteomics.	2017	eadme for [python] 2 and 3 v
28088763	r	Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R.	2017	e through [Bioconductor] at http:/
28088185	r	iGC-an integrated analysis package of gene expression and copy number alteration.	2017	tps://www.[Bioconductor].org/packa
28088176	r	TTCA: an R package for the identification of differentially expressed genes in time course microarray data.	2017	ttca: an [R package] for the i
28073760	r	Better diagnostic signatures from RNAseq data through use of auxiliary co-data.	2017	dge is an [R package] that incl
28073756	r	Feature selection using a one dimensional naïve Bayes' classifier increases the accuracy of support vector machine classification of CDR3 repertoires.	2017	tor . the [R package] e1071 is
28073755	r	Advanced Boolean modeling of biological networks applied to systems pharmacology.	2017	ent on r) [R package]. the resu
28069594	r	SigMod: an exact and efficient method to identify a strongly interconnected disease-associated module in a gene network.	2017	an [R package] sigmod is
28065917	r	Transformation and model choice for RNA-seq co-expression analysis.	2017	propose a [Bioconductor] package c
28065903	python	caspo: a toolbox for automated reasoning on the response of logical signaling networks families.	2017	oolbox, a [python] package i
28065901	java	RENT+: an improved method for inferring local genealogical trees from haplotypes with recombination.	2017	mented in [java], and is f
28065897	mathlab	TRFBA: an algorithm to integrate genome-scale metabolic and transcriptional regulatory networks with incorporation of expression data.	2017	mented in [matlab] software
28065895	java	Automated neuron tracing using probability hypothesis density filtering.	2017	en in the [java] programmi
28062444	mathlab	Robust parameter estimation for dynamical systems from outlier-corrupted data.	2017	the [matlab] implement
28062443	r	A novel non-parametric method for uncertainty evaluation of correlation-based molecular signatures: its application on PAM50 algorithm.	2017	n 'pbcmc' [R package] at biocon
28062442	perl	SINE_scan: an efficient tool to discover short interspersed nuclear elements (SINEs) in large-scale genomic datasets.	2017	mented in [perl] and suppo
28061750	java	GenomeCAT: a versatile tool for the analysis and integrative visualization of DNA copy number variants.	2017	tandalone [java] applicati
28057685	r	RImmPort: an R/Bioconductor package that enables ready-for-analysis immunology research data.	2017	platform [Bioconductor], to ensur
28057682	perl	phyloSkeleton: taxon selection, data retrieval and marker identification for phylogenomics.	2017	eton is a [perl] module an
28057677	r	PanViz: interactive visualization of the structure of functionally annotated pangenomes.	2017	companion [R package] that faci
28057677	javascript	PanViz: interactive visualization of the structure of functionally annotated pangenomes.	2017	tirely in [javascript] and is av
28056760	perl	MPD: multiplex primer design for next-generation targeted sequencing.	2017	g the mpd [perl] package p
28056760	javascript	MPD: multiplex primer design for next-generation targeted sequencing.	2017	rimers. a [javascript] web appli
28052927	r	DNABarcodes: an R package for the systematic construction of DNA sample tags.	2017	codes: an [R package] for the s
28049409	r	Negative binomial mixed models for analyzing microbiome count data.	2017	available [R package] bhglm ( h
28040696	mathlab	Parameter estimation for dynamical systems with discrete events and logical operations.	2017	advanced [matlab] interface
28039164	java	AltORFev facilitates the prediction of alternative open reading frames in eukaryotic mRNAs.	2017	eloped in [java] 1.8 using
28035030	java	CAME: identification of chromatin accessibility from nucleosome occupancy and methylome sequencing.	2017	mented in [java] and the p
28035029	r	geneAttribution: trait agnostic identification of candidate genes associated with noncoding variation.	2017	ution, an [R package] that assi
28035026	java	InMoDe: tools for learning and visualizing intra-motif dependencies of DNA binding sites.	2017	esent the [java] applicati
28035024	r	Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi.	2017	from the [Bioconductor] project.
28031185	r	MetaDCN: meta-analysis framework for differential co-expression network detection with an application in breast cancer.	2017	[R package] 'metadcn'
28031184	perl	SVScore: an impact prediction tool for structural variation.	2017	mented in [perl] and avail
28025202	java	Calypso: a user-friendly web-server for mining and visualizing microbiome-environment interactions.	2017	rammed in [java], perl and
28025202	r	Calypso: a user-friendly web-server for mining and visualizing microbiome-environment interactions.	2017	ava, perl [and R] and the s
28025202	perl	Calypso: a user-friendly web-server for mining and visualizing microbiome-environment interactions.	2017	in java, [perl] and r and
28025197	mathlab	A novel approach based on KATZ measure to predict associations of human microbiota with non-infectious diseases.	2017	[matlab] codes and
28025179	r	Measuring the diversity of the human microbiota with targeted next-generation sequencing.	2016	ilable an [R package], diversit
28011790	perl	High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE.	2017	c ++ and [perl] and is av
28011789	perl	myGenomeBrowser: building and sharing your own genome browser.	2017	mented in [perl], javascri
28011789	javascript	myGenomeBrowser: building and sharing your own genome browser.	2017	in perl, [javascript], apache a
28011787	r	switchde: inference of switch-like differential expression along single-cell trajectories.	2017	ompanying [R package] for ident
28011779	r	cerebroViz: an R package for anatomical visualization of spatiotemporal brain data.	2017	roviz: an [R package] for anato
28011775	r	MetaboSignal: a network-based approach for topological analysis of metabotype regulation via metabolic and signaling pathways.	2017	nal is an [R package] that allo
28011774	python	Fast motif matching revisited: high-order PWMs, SNPs and indels.	2017	0 and the [biopython] license (
28011773	r	ALTRE: workflow for defining ALTered Regulatory Elements using chromatin accessibility data.	2017	ents), an [R package] and assoc
28011770	python	Simulation-based estimation of branching models for LTR retrotransposons.	2017	ted using [python] software.
28007037	python	Block network mapping approach to quantitative trait locus analysis.	2016	mapping. [python] scripts a
28003266	python	GWAlpha: genome-wide estimation of additive effects (alpha) based on trait quantile distribution from pool-sequencing experiments.	2017	mented in [python], designed
28003264	r	A general framework for association analysis of microbial communities on a taxonomic tree.	2017	relevant [R package] milineage
28003263	r	bnstruct: an R package for Bayesian Network structure learning in the presence of missing data.	2017	truct: an [R package] for bayes
27998935	r	CymeR: cytometry analysis using KNIME, docker and R.	2017	e, docker [and R].
27998275	r	Efficient randomization of biological networks while preserving functional characterization of individual nodes.	2016	en-source [Bioconductor] package e
27993789	r	SPADEVizR: an R package for visualization, analysis and integration of SPADE results.	2017	evizr: an [R package] for visua
27993788	java	MRUniNovo: an efficient tool for de novo peptide sequencing utilizing the hadoop distributed computing framework.	2017	mented in [java]. the sour
27993787	bash	Improved VCF normalization for accurate VCF comparison.	2017	ban linux [bash] script al
27993786	python	DeFCoM: analysis and modeling of transcription factor binding sites using a motif-centric genomic footprinter.	2017	[python] code avai
27993779	java	Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks.	2017	er/ . the [java] code file
27993778	r	LEAP: constructing gene co-expression networks for single-cell RNA-sequencing data using pseudotime ordering.	2017	[R package] leap avai
27993774	r	KODAMA: an R package for knowledge discovery and data mining.	2017	odama: an [R package] for knowl
27993773	r	EGAD: ultra-fast functional analysis of gene networks.	2017	from the [Bioconductor] web site
27993773	mathlab	EGAD: ultra-fast functional analysis of gene networks.	2017	in r and [matlab]. the pack
27964719	javascript	Pathway collages: personalized multi-pathway diagrams.	2016	sent to a [javascript] pathway c
27938331	r	Robust multi-group gene set analysis with few replicates.	2016	nsive. an [R package] implement
27938328	perl	Combining independent de novo assemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms.	2016	a simple [perl] script) w
27927171	r	Finding an appropriate equation to measure similarity between binary vectors: case studies on Indonesian and Japanese herbal medicines.	2016	ons as an [R package] called bm
27923364	r	PCAN: phenotype consensus analysis to support disease-gene association.	2016	ity as an [R package] ( http://
27905885	python	MeFiT: merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing.	2016	mented in [python] and the s
27884103	python	ampliMethProfiler: a pipeline for the analysis of CpG methylation profiles of targeted deep bisulfite sequenced amplicons.	2016	ritten in [python] language
27832739	c++	libFLASM: a software library for fixed-length approximate string matching.	2016	en-source [C++] software
27814681	mathlab	WUFlux: an open-source platform for13C metabolic flux analysis of bacterial metabolism.	2016	nment) in [matlab], we built
27809781	mathlab	PSE-HMM: genome-wide CNV detection from NGS data using an HMM with Position-Specific Emission probabilities.	2016	ide cnvs. [matlab] programs
27797784	mathlab	BoostGAPFILL: improving the fidelity of metabolic network reconstructions through integrated constraint and pattern-based methods.	2017	[matlab] open sour
27797783	python	PyBoolNet: a python package for the generation, analysis and visualization of boolean networks.	2017	oolnet: a [python] package f
27797782	java	ImageJ-MATLAB: a bidirectional framework for scientific image analysis interoperability.	2017	ghtweight [java] library f
27797782	mathlab	ImageJ-MATLAB: a bidirectional framework for scientific image analysis interoperability.	2017	y between [matlab] and image
27797781	r	tcpl: the ToxCast pipeline for high-throughput screening data.	2017	the tcpl [R package] and its a
27797779	java	JADOPPT: java based AutoDock preparing and processing tool.	2017	jadoppt: [java] based aut
27797778	r	Network-based analysis of omics data: the LEAN method.	2017	ilable on [CRAN] ( https:/
27797777	python	INTEGRATE-neo: a pipeline for personalized gene fusion neoantigen discovery.	2017	c ++ and [python]. full sou
27797775	r	Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning.	2017	unk-db/ , [R package] to comput
27797772	r	ImpulseDE: detection of differentially expressed genes in time series data using impulse models.	2017	ede is an [R package] suited to
27797771	r	Imputing gene expression to maximize platform compatibility.	2017	able as a [R package] (affyimpu
27797767	r	miRNAmeConverter: an R/bioconductor package for translating mature miRNA names to different miRBase versions.	2017	conductor [R package] and web i
27797766	python	yMap: an automated method to map yeast variants to protein modifications and functional regions.	2017	present a [python] framework
27797763	python	Rabifier2: an improved bioinformatic classifier of Rab GTPases.	2017	from the [python] package i
27797762	perl	CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data.	2017	mented in [perl]. the sour
27797761	javascript	Isomorphic semantic mapping of variant call format (VCF2RDF).	2017	mented in [javascript], and was
27797760	r	Improving cross-study prediction through addon batch effect adjustment or addon normalization.	2017	ed in our [R package] bapred.
27797758	r	gsrc: an R package for genome structure rearrangement calling.	2017	gsrc: an [R package] for genom
27794558	r	Efficient detection of differentially methylated regions using DiMmeR.	2017	ogramming [language r], have no
27794557	python	FractBias: a graphical tool for assessing fractionation bias following polyploidy.	2017	able with [python] 2.7 or ip
27667792	r	Detecting subnetwork-level dynamic correlations.	2017	the [R package] is availa
27591080	r	signeR: an empirical Bayesian approach to mutational signature discovery.	2017	able as a [R package] at http:/
27793083	python	MEvoLib v1.0: the first molecular evolution library for Python.	2016	brary for [python].
27402908	mathlab	SYNBADm: a tool for optimization-based automated design of synthetic gene circuits.	2016	e popular [matlab] computati
27402905	python	PyPanda: a Python package for gene regulatory network reconstruction.	2016	ypanda: a [python] package f
27402900	r	samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files.	2016	roduce an [R package] called sa
27378304	r	MetaCycle: an integrated R package to evaluate periodicity in large scale data.	2016	ntegrated [R package] to evalua
27378300	r	An empirical Bayes method for genotyping and SNP detection using multi-sample next-generation sequencing data.	2016	ed in the [R package] ebgenotyp
27378295	mathlab	Unbiased classification of spatial strategies in the Barnes maze.	2016	nlab as a [matlab] applicati
27378292	java	ConsPred: a rule-based (re-)annotation framework for prokaryotic genomes.	2016	mented in [java], perl and
27378292	perl	ConsPred: a rule-based (re-)annotation framework for prokaryotic genomes.	2016	in java, [perl] and shell
27378290	r	TwoPhaseInd: an R package for estimating gene-treatment interactions and discovering predictive markers in randomized clinical trials.	2016	seind: an [R package] for estim
27784265	r	AlignStat: a web-tool and R package for statistical comparison of alternative multiple sequence alignments.	2016	-tool and [R package] for stati
27769170	r	dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data.	2016	pradar: a [Bioconductor] package f
27766961	python	VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements.	2016	n c++ and [python], for read
27766961	c++	VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements.	2016	ritten in [C++] and pytho
27766949	r	Improving sensitivity of linear regression-based cell type-specific differential expression deconvolution with per-gene vs. global significance threshold.	2016	ovide the [R package], lrcde, w
27766934	r	CC-PROMISE effectively integrates two forms of molecular data with multiple biologically related endpoints.	2016	the [R package] ccpromise
27760515	perl	Convert your favorite protein modeling program into a mutation predictor: MODICT .	2016	he modict [perl] package a
27756200	r	Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries.	2016	ithm in a [Bioconductor] package t
27742697	python	Visualizing the geography of genetic variants.	2017	q_api/ ). [python] and javas
27742697	javascript	Visualizing the geography of genetic variants.	2017	ython and [javascript] source co
27733121	r	Extending digital PCR analysis by modelling quantification cycle data.	2016	en source [language r] has been
27717304	java	Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers.	2016	mented in [java] and uses
27716034	r	VennDiagramWeb: a web application for the generation of highly customizable Venn and Euler diagrams.	2016	nndiagram [R package]. venndiag
27694195	r	Combining multiple tools outperforms individual methods in gene set enrichment analyses.	2017	ble as an [R package] at http:/
27677958	r	Rare variant association test in family-based sequencing studies.	2017	ted in an [R package] 'gskat',
27667791	java	LongISLND: in silico sequencing of lengthy and noisy datatypes.	2016	mented in [java] and avail
27667790	java	cMapper: gene-centric connectivity mapper for EBI-RDF platform.	2017	ped using [java] and deplo
27663497	perl	AcCNET (Accessory Genome Constellation Network): comparative genomics software for accessory genome analysis using bipartite networks.	2017	ork) is a [perl] applicati
27659774	javascript	MicroScope: ChIP-seq and RNA-seq software analysis suite for gene expression heatmaps.	2016	on the d3 [javascript] library:
27659451	r	PSSV: a novel pattern-based probabilistic approach for somatic structural variation identification.	2017	an [R package] of pssv i
27651481	r	AlloMap6: an R package for genetic linkage analysis in allohexaploids.	2017	omap6: an [R package] for genet
27650223	r	systemPipeR: NGS workflow and report generation environment.	2016	tems from [Bioconductor] ( http://
27634949	perl	Verdant: automated annotation, alignment and phylogenetic analysis of whole chloroplast genomes.	2017	d in php, [perl], mysql, j
27634949	javascript	Verdant: automated annotation, alignment and phylogenetic analysis of whole chloroplast genomes.	2017	l, mysql, [javascript], html and
27634947	r	IsotopicLabelling: an R package for the analysis of MS isotopic patterns of labelled analytes.	2017	lling: an [R package] for the a
27634135	python	Development of a prediction system for tail-anchored proteins.	2016	ritten in [python] is availa
27618863	python	Tissue enrichment analysis for C. elegans genomics.	2016	ded using [python]'s standar
27616707	mathlab	DM-BLD: differential methylation detection using a hierarchical Bayesian model exploiting local dependency.	2017	a [matlab] package o
27614350	java	Assessment of cancer and virus antigens for cross-reactivity in human tissues.	2017	nted as a [java] program,
27605107	mathlab	BeReTa: a systematic method for identifying target transcriptional regulators to enhance microbial production of chemicals.	2017	[matlab] code is a
27605105	java	ReliableGenome: annotation of genomic regions with high/low variant calling concordance.	2017	mented in [java], source c
27605102	java	PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods.	2017	dependent [java] tool that
27605100	python	MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments.	2017	mented in [python], perl and
27605100	perl	MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments.	2017	n python, [perl] and javas
27605100	javascript	MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments.	2017	perl and [javascript] and is fr
27605099	java	OntoBrowser: a collaborative tool for curation of ontologies by subject matter experts.	2017	run on a [java] ee applic
27605098	r	DAPAR & ProStaR: software to perform statistical analyses in quantitative discovery proteomics.	2017	ed in the [R language] and are a
27597310	r	NEAT: an efficient network enrichment analysis test.	2016	ed in the [R package] neat, whi
27592708	r	Gene- and pathway-based association tests for multiple traits with GWAS summary statistics.	2017	mented in [R package] aspu, fre
27591081	r	Precrec: fast and accurate precision-recall and ROC curve calculations in R.	2017	able from [CRAN] (https://
27587701	python	Bayesian parameter estimation for the Wnt pathway: an infinite mixture models approach.	2016	[python] scripts f
27587695	r	Large-scale inference of conjunctive Bayesian networks.	2016	ted as an [R package] available
27587694	mathlab	L1 regularization facilitates detection of cell type-specific parameters in dynamical systems.	2016	a [matlab] implement
27587693	python	A probabilistic model for detecting rigid domains in protein structures.	2016	the [python] source co
27587690	python	Patterns of amino acid conservation in human and animal immunodeficiency viruses.	2016	a [python] package i
27587680	r	A unified model based multifactor dimensionality reduction framework for detecting gene-gene interactions.	2016	a [R package] ummdr a
27587666	java	PanTools: representation, storage and exploration of pan-genomic data.	2016	the [java] implement
27587664	java	The Network Library: a framework to rapidly integrate network biology resources.	2016	eloped in [java] and avail
27587659	python	Combining dependent P-values with an empirical adaptation of Brown's method.	2016	ilable in [python], r, and m
27587659	r	Combining dependent P-values with an empirical adaptation of Brown's method.	2016	able as a [Bioconductor] package f
27587659	mathlab	Combining dependent P-values with an empirical adaptation of Brown's method.	2016	n, r, and [matlab] and can b
27587657	r	TANDEM: a two-stage approach to maximize interpretability of drug response models based on multiple molecular data types.	2016	ble as an [R package] on cran (
27585881	r	Risk-conscious correction of batch effects: maximising information extraction from high-throughput genomic datasets.	2016	lly as an [R package] ( https:/
27585881	mathlab	Risk-conscious correction of batch effects: maximising information extraction from high-throughput genomic datasets.	2016	compiled [matlab] package (
27578804	python	FATSLiM: a fast and robust software to analyze MD simulations of membranes.	2017	ritten in [python]. source c
27565584	java	A likelihood ratio-based method to predict exact pedigrees for complex families from next-generation sequencing data.	2017	a [java] standalon
27559155	mathlab	Fast-SNP: a fast matrix pre-processing algorithm for efficient loopless flux optimization of metabolic models.	2016	code for [matlab] including
27559153	c	Discoal: flexible coalescent simulations with selection.	2016	ed in the [C programming] language.
27553625	mathlab	Stepwise iterative maximum likelihood clustering approach.	2016	ethods. a [matlab] package o
27553489	r	Interpreting transcriptional changes using causal graphs: new methods and their practical utility on public networks.	2016	od in the [R package] quaternar
27543791	r	Robust logistic regression to narrow down the winner's curse for rare and recessive susceptibility variants.	2017	ended the [R package] 'robustba
27542772	r	STAMS: STRING-assisted module search for genome wide association studies and application to autism.	2016	ted as an [R package] and is fr
27542771	python	MSIdV: a versatile tool to visualize biological indices from mass spectrometry imaging data.	2016	mented in [python] 2.7 and i
27542770	r	DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq experiments.	2016	esubs: an [R package] for flexi
27534850	r	A machine learning strategy for predicting localization of post-translational modification sites in protein-protein interacting regions.	2016	plemented [R package] is availa
27522082	r	oxBS-MLE: an efficient method to estimate 5-methylcytosine and 5-hydroxymethylcytosine in paired bisulfite and oxidative bisulfite treated DNA.	2016	mented in [Bioconductor] package e
27522081	javascript	Gene Slider: sequence logo interactive data-visualization for education and research.	2016	mented in [javascript] and proce
27516195	python	BAMQL: a query language for extracting reads from BAM files.	2016	pysam for [python]. both all
27516195	perl	BAMQL: a query language for extracting reads from BAM files.	2016	tools for [perl] and pysam
27515739	python	LCA*: an entropy-based measure for taxonomic assignment within assembled metagenomes.	2016	and-alone [python] library c
27515738	r	NVT: a fast and simple tool for the assessment of RNA-seq normalization strategies.	2016	the [R package] is freely
27503227	perl	SRinversion: a tool for detecting short inversions by splitting and re-aligning poorly mapped and unmapped sequencing reads.	2016	mented in [perl] and is pu
27503226	r	shinyGEO: a web-based application for analyzing gene expression omnibus datasets.	2016	ta export [and R] code gene
27503224	python	PathScore: a web tool for identifying altered pathways in cancer data.	2016	mented in [python] and mysql
27503223	r	Bayesian network feature finder (BANFF): an R package for gene network feature selection.	2016	anff): an [R package] for gene
27497442	r	A novel copy number variants kernel association test with application to autism spectrum disorders studies.	2016	a [R package] to implem
27497440	r	scphaser: haplotype inference using single-cell RNA-seq data.	2016	haser, an [R package] that phas
27497439	python	genipe: an automated genome-wide imputation pipeline with automatic reporting and statistical tools.	2016	en source [python] software
27493193	perl	FARAO: the flexible all-round annotation organizer.	2016	mented in [perl] and is su
27480116	r	Gene, Environment and Methylation (GEM): a tool suite to efficiently navigate large scale epigenome wide association studies and integrate genotype and interaction between genotype and environment.	2016	ts. it is [written in R] code and
27473172	r	RevEcoR: an R package for the reverse ecology analysis of microbiomes.	2016	vecor: an [R package] for the r
27466625	mathlab	Joint sparse canonical correlation analysis for detecting differential imaging genetics modules.	2016	the [matlab] code is a
27465477	r	flowVS: channel-specific variance stabilization in flow cytometry.	2016	ilable in [Bioconductor].
27454116	mathlab	A systematic framework to derive N-glycan biosynthesis process and the automated construction of glycosylation networks.	2016	tworks in [matlab] with the
27436563	r	Variance adaptive shrinkage (vash): flexible empirical Bayes estimation of variances.	2016	ted in an [R package] vashr ava
27412096	javascript	MSAViewer: interactive JavaScript visualization of multiple sequence alignments.	2016	teractive [javascript] visualiza
27370569	r	MethPed: an R package for the identification of pediatric brain tumor subtypes.	2016	thped: an [R package] for the i
27363390	perl	A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies.	2016	ped using [perl], bioperl
27357171	r	Estimating and testing high-dimensional mediation effects in epigenetic studies.	2016	[R package], source c
27357170	r	Network-based pathway enrichment analysis with incomplete network information.	2016	ilable on [CRAN].
27354701	python	CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets.	2016	ritten in [python], builds o
27354695	r	ABAEnrichment: an R package to test for gene set expression enrichment in the adult and developing human brain.	2016	hment: an [R package] to test f
27342648	mathlab	TRaCE+: Ensemble inference of gene regulatory networks from transcriptional expression profiles of gene knock-out experiments.	2016	tines for [matlab] are freel
27342194	java	EmpPrior: using outside empirical data to inform branch-length priors for Bayesian phylogenetics.	2016	ritten in [java] to query
27342194	r	EmpPrior: using outside empirical data to inform branch-length priors for Bayesian phylogenetics.	2016	rior-fit, [written in R] to parame
27341818	r	Exploiting expression patterns across multiple tissues to map expression quantitative trait loci.	2016	ithin the [R package] jaguar, w
27334476	r	SERAPHIM: studying environmental rasters and phylogenetically informed movements.	2016	ox.ac.uk/ [R package], source c
27334471	perl	CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs.	2016	mented in [perl], mysql an
27334001	r	multiDE: a dimension reduced model based statistical method for differential expression analysis using RNA-sequencing data with multiple treatment conditions.	2016	thods. an [R package] implement
27333889	r	Generalized enrichment analysis improves the detection of adverse drug events from the biomedical literature.	2016	rovide an [R package] for explo
27324198	python	RTCR: a pipeline for complete and accurate recovery of T cell repertoires from high throughput sequencing data.	2016	mented in [python] (v2.7) an
27324197	r	Integrated gene set analysis for microRNA studies.	2016	ed in the [Bioconductor] library m
27323392	r	compendiumdb: an R package for retrieval and storage of functional genomics data.	2016	iumdb: an [R package] for retri
27323392	perl	compendiumdb: an R package for retrieval and storage of functional genomics data.	2016	mysql and [perl]. source c
27318208	python	Statistical modeling of isoform splicing dynamics from RNA-seq time series data.	2016	[python] code is f
27318205	r	NegGOA: negative GO annotations selection using ontology structure.	2016	he matlab [and R] codes are
27318205	mathlab	NegGOA: negative GO annotations selection using ontology structure.	2016	the [matlab] and r cod
27318203	perl	The structural effects of mutations can aid in differential phenotype prediction of beta-myosin heavy chain (Myosin-7) missense variants.	2016	mented in [perl] and c and
27318199	python	TADtool: visual parameter identification for TAD-calling algorithms.	2016	n or as a [python] package f
27318198	r	Pseudotime estimation: deconfounding single cell time series.	2016	ilable on [CRAN] in the de
27316337	r	PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq.	2016	e with an [R package], assigned
27312412	perl	RADIS: analysis of RAD-seq data for interspecific phylogeny.	2016	oduce the [perl] pipeline
27312411	python	MultiQC: summarize analysis results for multiple tools and samples in a single report.	2016	thub, the [python] package i
27312410	java	ARGON: fast, whole-genome simulation of the discrete time Wright-fisher process.	2016	ritten in [java], open sou
27307645	java	BioASF: a framework for automatically generating executable pathway models specified in BioPAX.	2016	mented in [java], is open
27307638	c	RNAiFold2T: Constraint Programming design of thermo-IRES switches.	2016	ftware is [written in C] ++ and us
27307630	r	Linear effects models of signaling pathways from combinatorial perturbation data.	2016	able as a [R package] at http:/
27307614	c	deBWT: parallel construction of Burrows-Wheeler Transform for large collection of genomes with de Bruijn-branch encoding.	2016	mented in [C language], the sour
27307611	mathlab	Analysis of differential splicing suggests different modes of short-term splicing regulation.	2016	r and [matlab] codes imp
27307610	r	A cross-species bi-clustering approach to identifying conserved co-regulated genes.	2016	the [R package] containin
27307609	python	Influence maximization in time bounded network identifies transcription factors regulating perturbed pathways.	2016	mented in [python] and avail
27296983	mathlab	A time-varying group sparse additive model for genome-wide association studies of dynamic complex traits.	2016	mented in [matlab].
27296982	r	GSA-Lightning: ultra-fast permutation-based gene set analysis.	2016	lightning [R package] is availa
27296981	r	CONDOP: an R package for CONdition-Dependent Operon Predictions.	2016	ondop: an [R package] for condi
27296979	java	Web-based network analysis and visualization using CellMaps.	2016	in c and [java].
27296979	javascript	Web-based network analysis and visualization using CellMaps.	2016	available [javascript] api.
27295045	r	Inferring active regulatory networks from gene expression data using a combination of prior knowledge and enrichment analysis.	2016	ted as an [R package], currentl
27288501	r	RareVariantVis: new tool for visualization of causative variants in rare monogenic disorders using whole genome sequencing data.	2016	tps://www.[Bioconductor].org/packa
27288499	r	GenVisR: Genomic Visualizations in R.	2016	isr is an [R package] available
27288495	r	Inferring the perturbation time from biological time course data.	2016	ion: : an [R package], detime,
27288494	r	bdvis: visualizing biodiversity data in R.	2016	scribe an [R package], bdvis, w
27288492	r	Zerone: a ChIP-seq discretizer for multiple replicates with built-in quality control.	2016	and as an [R package]. the c so
27283952	java	TaggerOne: joint named entity recognition and normalization with semi-Markov Models.	2016	gerone, a [java] implement
27283951	r	GHap: an R package for genome-wide haplotyping.	2016	ghap: an [R package] for genom
27283948	python	pong: fast analysis and visualization of latent clusters in population genetic data.	2016	using the [python] package m
27273669	r	R.JIVE for exploration of multi-source molecular data.	2016	intuitive [R package] to perfor
27266441	r	HDTD: analyzing multi-tissue gene expression data.	2016	the [R package] hdtd is p
27259541	java	MetaFast: fast reference-free graph-based comparison of shotgun metagenomic data.	2016	ritten in [java] and is pl
27256314	r	RANKS: a flexible tool for node label ranking and classification in biological networks.	2016	ackage is [written in R], except f
27230384	javascript	Crowdsourcing the nodulation gene network discovery environment.	2016	nd vis.js [javascript] libraries
27207944	r	Differential rhythmicity: detecting altered rhythmicity in biological data.	2016	ilable on [CRAN].
27207943	r	Complex heatmaps reveal patterns and correlations in multidimensional genomic data.	2016	from the [Bioconductor] project:
27187204	r	seqlm: an MDL based method for identifying differentially methylated regions in high density methylation array data.	2016	mented in [R package] seqlm tha
27153821	perl	DensityMap: a genome viewer for illustrating the densities of features.	2016	ghtweight [perl] program t
27153725	python	NMRPro: an integrated web component for interactive processing and visualization of NMR spectra.	2016	parts: a [python] package t
27153719	r	MetaKTSP: a meta-analytic top scoring pair method for robust cross-study validation of omics prediction analysis.	2016	an [R package] metaktsp
27153717	python	FRED 2: an immunoinformatics framework for Python.	2016	ework for [python].
27153716	java	Multiple structure single parameter: analysis of a single protein nano environment descriptor characterizing a shared loci on structurally aligned proteins.	2016	in perl, [java] and javas
27153716	perl	Multiple structure single parameter: analysis of a single protein nano environment descriptor characterizing a shared loci on structurally aligned proteins.	2016	mented in [perl], java and
27153716	javascript	Multiple structure single parameter: analysis of a single protein nano environment descriptor characterizing a shared loci on structurally aligned proteins.	2016	java and [javascript] and jmol
27153715	r	cit: hypothesis testing software for mediation analysis in genomic applications.	2016	en-source [R package] is freely
27153711	mathlab	Simulated single molecule microscopy with SMeagol.	2016	l runs on [matlab] r2014 and
27153705	mathlab	KiT: a MATLAB package for kinetochore tracking.	2016	kit: a [matlab] package f
27153704	r	A web application for sample size and power calculation in case-control microbiome studies.	2016	erface is [written in R] code usin
27153702	c	SweepFinder2: increased sensitivity, robustness and flexibility.	2016	e that is [written in C] and can b
27153696	mathlab	ll-ACHRB: a scalable algorithm for sampling the feasible solution space of metabolic networks.	2016	code for [matlab] and octav
27153692	java	Reaction Decoder Tool (RDT): extracting features from chemical reactions.	2016	mented in [java], supporte
27153684	r	solarius: an R interface to SOLAR for variance component analysis in pedigrees.	2016	ilable on [CRAN] and on gi
27153679	r	Coala: an R framework for coalescent simulation.	2016	coala, an [R package] for calli
27153677	r	Assessing statistical significance in multivariable genome wide association analysis.	2016	en-source [Bioconductor] package h
27153673	python	Goldilocks: a tool for identifying genomic regions that are 'just right'.	2016	ilocks: a [python] package p
27153672	r	RCP: a novel probe design bias correction method for Illumina Methylation BeadChip.	2016	into the [R package] enmix, wh
27153665	python	DOGMA: domain-based transcriptome and proteome quality assessment.	2016	mented in [python] and publi
27153664	mathlab	Combenefit: an interactive platform for the analysis and visualization of drug combinations.	2016	ided as a [matlab] package b
27153663	python	MEANS: python package for Moment Expansion Approximation, iNference and Simulation.	2016	means: [python] package f
27153661	r	densityCut: an efficient and versatile topological approach for automatic clustering of biological data.	2016	ensitycut [R package] is availa
27153657	mathlab	Spectral identification of topological domains.	2016	the [matlab] source co
27153654	python	rnaQUAST: a quality assessment tool for de novo transcriptome assemblies.	2016	mented in [python] and is fr
27153652	java	ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information.	2016	a [java] cross-pla
27153646	javascript	TnT: a set of libraries for visualizing trees and track-based annotations for the web.	2016	ritten in [javascript], licensed
27153645	r	Romulus: robust multi-state identification of transcription factor binding sites from DNase-seq data.	2016	ble as an [R package] at http:/
27153642	r	Pasha: a versatile R package for piling chromatin HTS data.	2016	versatile [R package] for pilin
27153639	r	gkmSVM: an R package for gapped-kmer SVM.	2016	kmsvm: an [R package] for gappe
27153638	r	Beta-Poisson model for single-cell RNA-seq data analyses.	2016	an [R package] bpsc for
27153635	r	TreeQTL: hierarchical error control for eQTL findings.	2016	the [R package] treeqtl i
27153632	c	hotspot: software to support sperm-typing for investigating recombination hotspots.	2016	otspot is [written in C]. sources
27153628	r	flowAI: automatic and interactive anomaly discerning tools for flow cytometry data.	2016	resent an [R package], flowai,
27153627	mathlab	MEMO: multi-experiment mixture model analysis of censored data.	2016	mented in [matlab] and freel
27153626	python	Tools4miRs - one place to gather all the tools for miRNA analysis.	2016	mented in [python] using dja
27153620	python	MOCAT2: a metagenomic assembly, annotation and profiling framework.	2016	erl 5 and [python] 2.7, desi
27153620	perl	MOCAT2: a metagenomic assembly, annotation and profiling framework.	2016	mented in [perl] 5 and pyt
27153619	python	ProtPOS: a python package for the prediction of protein preferred orientation on a surface.	2016	rotpos: a [python] package f
27153616	python	SBtab: a flexible table format for data exchange in systems biology.	2016	and-alone [python] code cont
27153616	r	SBtab: a flexible table format for data exchange in systems biology.	2016	l, matlab [and R]. the stan
27153616	mathlab	SBtab: a flexible table format for data exchange in systems biology.	2016	ms excel, [matlab] and r. th
27153605	javascript	pileup.js: a JavaScript library for interactive and in-browser visualization of genomic data.	2016	eup.js: a [javascript] library f
27153599	r	HilbertCurve: an R/Bioconductor package for high-resolution visualization of genomic data.	2016	from the [Bioconductor] project:
27153598	r	FREGAT: an R package for region-based association analysis.	2016	regat: an [R package] for regio
27153596	r	OxyBS: estimation of 5-methylcytosine and 5-hydroxymethylcytosine from tandem-treated oxidative bisulfite and bisulfite DNA.	2016	ybs is an [R package] available
27153595	python	MGEScan: a Galaxy-based system for identifying retrotransposons in genomes.	2016	h mpi and [python] threading
27153592	r	Characterizing gene sets using discriminative random walks with restart on heterogeneous biological networks.	2016	ted as an [R package] available
27153588	java	Ferret: a user-friendly Java tool to extract data from the 1000 Genomes Project.	2016	-friendly [java] tool to e
27153587	python	jSplice: a high-performance method for accurate prediction of alternative splicing events and its application to large-scale renal cancer transcriptome data.	2016	tandalone [python] applicati
27153585	r	EBglmnet: a comprehensive R package for sparse generalized linear regression models.	2016	rehensive [R package] for spars
27153580	r	chromPlot: visualization of genomic data in chromosomal context.	2016	ttp://www.[Bioconductor].org
27153579	perl	ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database.	2016	[perl] script fo
27153577	mathlab	Analysis of CFSE time-series data using division-, age- and label-structured population models.	2016	the [matlab] source co
27153575	python	mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories.	2016	c ++ and [python], and supp
27153574	r	SNPhood: investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data.	2016	conductor [R package] to invest
27153572	javascript	Visual Omics Explorer (VOE): a cross-platform portal for interactive data visualization.	2016	html and [javascript] code. voe
27146037	r	readat: An R package for reading and working with SomaLogic ADAT files.	2016	eadat: an [R package] for readi
27143038	javascript	QUADrATiC: scalable gene expression connectivity mapping for repurposing FDA-approved therapeutics.	2016	advanced [javascript] framework
27117841	mathlab	eSTGt: a programming and simulation environment for population dynamics.	2016	or using [matlab]'s command
27113060	r	Erratum to: 'CompGO: an R package for comparing and visualizing Gene Ontology enrichment differences between DNA binding experiments'.	2016	ompgo: an [R package] for compa
27094401	r	Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves.	2016	urver: an [R package] for obtai
27083325	python	UNDR ROVER - a fast and accurate variant caller for targeted DNA sequencing.	2016	mented in [python] and runs
27071656	python	Implementation of a methodology for determining elastic properties of lipid assemblies from molecular dynamics simulations.	2016	a set of [python] modules u
27059780	java	CollapsABEL: an R library for detecting compound heterozygote alleles in genome-wide association studies.	2016	ncy using [java] or c++. i
27059780	c++	CollapsABEL: an R library for detecting compound heterozygote alleles in genome-wide association studies.	2016	g java or [C++]. intermed
27059780	r	CollapsABEL: an R library for detecting compound heterozygote alleles in genome-wide association studies.	2016	on in the [R package] collapsab
27044654	java	The systems biology format converter.	2016	ritten in [java] and can b
27044654	mathlab	The systems biology format converter.	2016	sbgn-ml, [matlab], octave,
27029470	r	Sample size calculation while controlling false discovery rate for differential expression analysis with RNA-sequencing experiments.	2016	rovide an [R package] ssizerna
27005934	r	caOmicsV: an R package for visualizing multidimensional cancer genomic data.	2016	micsv: an [R package] for visua
27001666	r	Leveraging protein quaternary structure to identify oncogenic driver mutations.	2016	eins. the [R package] is availa
26968614	r	GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data.	2016	standard [Bioconductor] extension
26964749	mathlab	PeTTSy: a computational tool for perturbation analysis of complex systems biology models.	2016	ckage for [matlab] which imp
26961892	r	FastPop: a rapid principal component derived method to infer intercontinental ancestry using genetic data.	2016	efficient [R package] that fill
26961516	perl	Geena 2, improved automated analysis of MALDI/TOF mass spectra.	2016	n php and [perl]. input an
26956433	r	Improving cell mixture deconvolution by identifying optimal DNA methylation libraries (IDOL).	2016	(2)>0.90 [and R] m s e<4.0
26951498	r	Testing for association between RNA-Seq and high-dimensional data.	2016	sion. the [R package] globalseq
26873932	java	An empirical Bayes change-point model for identifying 3' and 5' alternative splicing by next-generation RNA sequencing.	2016	mented in [java] and can b
26861823	python	Predicting physiologically relevant SH3 domain mediated protein-protein interactions in yeast.	2016	ted using [python] 2.7 and c
26861822	r	Measuring the spatial correlations of protein binding sites.	2016	an [R package] is availa
26861821	r	TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data.	2016	ronco: an [R package] for the i
26861819	mathlab	MOCCASIN: converting MATLAB ODE models to SBML.	2016	onverting [matlab] ode model
26860319	r	LowMACA: exploiting protein family analysis for the identification of rare driver mutations in cancer.	2016	aca is an [R package] available
26860128	r	Analysing multiple types of molecular profiles simultaneously: connecting the needles in the haystack.	2016	a the sim [Bioconductor] package.
26833345	r	GiANT: gene set uncertainty in enrichment analysis.	2016	ilable on [CRAN].
26833343	mathlab	Model-based media selection to minimize the cost of metabolic cooperation in microbial ecosystems.	2016	able as a [matlab] script in
26833341	mathlab	Integrative analysis for identifying joint modular patterns of gene-expression and drug-response data.	2016	a [matlab] package o
26830926	python	ClinQC: a tool for quality control and cleaning of Sanger and NGS data in clinical research.	2016	ritten in [python] with mult
26819473	javascript	BioCircos.js: an interactive Circos JavaScript library for biological data visualization on web applications.	2016	ve circos [javascript] library f
26819470	r	Differential methylation analysis for BS-seq data under general experimental design.	2016	ilable as [Bioconductor] package d
26819469	python	FILTUS: a desktop GUI for fast and efficient detection of disease-causing variants, including a novel autozygosity detector.	2016	ritten in [python] and runs
26819101	javascript	DNAism: exploring genomic datasets on the web with Horizon Charts.	2016	existing [javascript] library (
26818685	r	A full Bayesian partition model for identifying hypo- and hyper-methylated loci from single nucleotide resolution sequencing data.	2016	lysis. an [R package] named as
26803162	r	DesignSignatures: a tool for designing primers that yields amplicons with distinct signatures.	2016	able from [Bioconductor].
26803161	r	PAA: an R/bioconductor package for biomarker discovery with protein microarrays.	2016	ttp://www.[Bioconductor].org/packa
26803158	r	FamAgg: an R package to evaluate familial aggregation of traits in large pedigrees.	2016	amagg: an [R package] to evalua
26803157	r	lodGWAS: a software package for genome-wide association analysis of biomarkers with a limit of detection.	2016	sy-to-use [R package] that prov
26801960	mathlab	Structured sparse canonical correlation analysis for brain imaging genetics: an improved GraphNet method.	2016	the [matlab] code and
26794317	perl	The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries.	2016	xtensible [perl] library w
26794315	r	TFBSTools: an R/bioconductor package for transcription factor binding site analysis.	2016	from the [Bioconductor] website (
26791995	r	Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis.	2016	[Bioconductor]'s enrichm
26787665	r	Sampletrees and Rsampletrees: sampling gene genealogies conditional on SNP genotype data.	2016	.html the [R package] rsampletr
26773132	perl	SIRAH tools: mapping, backmapping and visualization of coarse-grained models.	2016	ritten in [perl], tcl, or
26772743	c++	A computational method for genotype calling in family-based sequencing data.	2016	ntly in a [C++] program f
26769317	python	Realizing privacy preserving genome-wide association studies.	2016	a [python] implement
26757899	python	Aligning the unalignable: bacteriophage whole genome alignments.	2016	trains. a [python] implement
26755624	python	Computational discovery of pathway-level genetic vulnerabilities in non-small-cell lung cancer.	2016	mented in [python] and is fr
26753519	r	Combining location-and-scale batch effect adjustment with data cleaning by latent factor adjustment.	2016	es in the [R package] bapred av
26743507	r	OEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data.	2016	ble as an [R package] along wit
26733452	r	Path2PPI: an R package to predict protein-protein interaction networks for a set of proteins.	2016	h2ppi: an [R package] to predic
26729218	java	Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks.	2016	en-source [java] library a
26708336	r	rCGH: a comprehensive array-based genomic profile platform for precision medicine.	2016	the rcgh [R package] is availa
26708334	javascript	HitWalker2: visual analytics for precision medicine and beyond.	2016	neo4j and [javascript] (d3.js an
26685309	mathlab	Fast integration-based prediction bands for ordinary differential equation models.	2016	based on [matlab] and freel
26685307	r	traseR: an R package for performing trait-associated SNP enrichment analysis in genomic intervals.	2016	raser: an [R package] for perfo
26685306	r	PaxtoolsR: pathway analysis in R using Pathway Commons.	2016	conductor [R package] repositor
26685305	mathlab	FluxModeCalculator: an efficient tool for large-scale flux mode computation.	2016	ration in [matlab], called f
26677932	python	PCTFPeval: a web tool for benchmarking newly developed algorithms for predicting cooperative transcription factor pairs in yeast.	2015	n php and [python] programmi
26668005	r	DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding.	2016	ogramming [language r] and is fr
26656933	c	BioFVM: an efficient, parallelized diffusive transport solver for 3-D biological simulations.	2016	biofvm is [written in C] ++ with p
26656932	python	Sequence database versioning for command line and Galaxy bioinformatics servers.	2016	ritten in [python] and relea
26656570	r	Adaptive gene- and pathway-trait association testing with GWAS summary statistics.	2016	mented in [R package] aspu, fre
26656004	r	PharmacoGx: an R package for analysis of large pharmacogenomic datasets.	2016	acogx: an [R package] for analy
26652794	java	MRMPlus: an open source quality control and assessment tool for SRM/MRM assay development.	2015	dependent [java] programin
26644415	java	Joint detection of copy number variations in parent-offspring trios.	2016	nation of [java] and r is
26644415	r	Joint detection of copy number variations in parent-offspring trios.	2016	n of java [and R] is freely
26637292	c	Maligner: a fast ordered restriction map aligner.	2016	ftware is [written in C] ++ and is
26635141	r	rcellminer: exploring molecular profiles and drug response of the NCI-60 cell lines in R.	2016	cellminer [R package] provides
26628587	mathlab	IKAP: A heuristic framework for inference of kinase activities from Phosphoproteomics data.	2016	mented in [matlab] and be do
26607490	r	Genefu: an R/Bioconductor package for computation of gene expression-based signatures in breast cancer.	2016	able from [Bioconductor]. http://w
26589280	c++	hybridSPAdes: an algorithm for hybrid assembly of short and long reads.	2016	mented in [C++] as a part
26589278	r	Reliable ABC model choice via random forests.	2016	ed in the [R package] abcrf ava
26589277	python	SomVarIUS: somatic variant identification from unpaired tissue samples.	2016	ritten in [python] 2.7 and a
26589276	perl	ParTIES: a toolbox for Paramecium interspersed DNA elimination studies.	2016	-threaded [perl] software
26589275	python	FoCuS-point: software for STED fluorescence correlation and time-gated single photon counting.	2016	ritten in [python] and is av
26589274	r	LocusExplorer: a user-friendly tool for integrated visualization of human genetic association data and biological annotations.	2016	plorer is [written in R] using the
26589273	mathlab	CellTracker (not only) for dummies.	2016	ritten in [matlab] (the math
26577052	r	DiffLogo: a comparative visualization of sequence motifs.	2015	-friendly [R package] for visua
26568633	python	Optimal design of gene knockout experiments for gene regulatory network inference.	2016	atlab and [python] scripts o
26568633	mathlab	Optimal design of gene knockout experiments for gene regulatory network inference.	2016	[matlab] and pytho
26568624	c++	Optimal seed solver: optimizing seed selection in read mapping.	2016	solver in [C++] at: https
26558877	c	Two molecular measures of relatedness based on haplotype sharing.	2015	founders. [using C] in linear
26556386	r	contamDE: differential expression analysis of RNA-seq data for contaminated tumor samples.	2016	an [R package] contamde
26556385	r	Specific identification and quantification of circular RNAs from sequencing data.	2016	ns by our [R package] circtest
26556383	java	Realtime analysis and visualization of MinION sequencing data with npReader.	2016	ritten in [java] and is fr
26553913	r	CopyNumber450kCancer: baseline correction for accurate copy number calling from the 450k methylation array.	2016	ted as an [R package]. the pack
26552737	java	From raw data to data-analysis for magnetic resonance spectroscopy--the missing link: jMRUI2XML.	2015	2xml is a [java] solution
26545824	python	Automatic generation of bioinformatics tools for predicting protein-ligand binding sites.	2016	mented in [python] and suppo
26545822	r	Comparison of genetic variants in matched samples using thesaurus annotation.	2016	ted in an [R package] available
26545820	r	Probabilistic models of genetic variation in structured populations applied to global human studies.	2016	conductor [R package] called lf
26543176	mathlab	Shape component analysis: structure-preserving dimension reduction on biological shape spaces.	2016	s made in [matlab] and suppo
26543171	r	TESS: an R package for efficiently simulating phylogenetic trees and performing Bayesian inference of lineage diversification rates.	2016	tess: an [R package] for effic
26538306	python	Fizzy: feature subset selection for metagenomics.	2015	ped a new [python] command l
26537733	c++	BitTorious volunteer: server-side extensions for centrally-managed volunteer storage in BitTorrent swarms.	2015	ovided in [C++] for infor
26537417	python	ODTbrain: a Python library for full-view, dense diffraction tomography.	2015	tbrain: a [python] library f
26530724	python	PHYLUCE is a software package for the analysis of conserved genomic loci.	2016	itten for [python] 2.7. phyl
26520854	java	Enumeration and extension of non-equivalent deterministic update schedules in Boolean networks.	2016	m made in [java] and the f
26519502	r	Bayesian inference with historical data-based informative priors improves detection of differentially expressed genes.	2016	mented in [R package] ipbt, whi
26515826	javascript	Protael: protein data visualization library for the web.	2016	tael is a [javascript] library f
26515824	c++	SeqSIMLA2_exact: simulate multiple disease sites in large pedigrees with given disease status for diseases with low prevalence.	2016	nted with [C++] and is av
26515822	perl	PRIMUS: improving pedigree reconstruction using mitochondrial and Y haplotypes.	2016	pdates in [perl] and it is
26515818	r	EMDomics: a robust and powerful method for the identification of genes differentially expressed between heterogeneous classes.	2016	the [R package] is availa
26514335	r	ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data.	2015	paseq: an [R package] for topol
26508760	r	RVFam: an R package for rare variant association analysis with family data.	2016	rvfam: an [R package] for rare
26508757	r	LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor.	2016	[R package] available
26508755	r	caRpools: an R package for exploratory data analysis and documentation of pooled CRISPR/Cas9 screens.	2016	pools: an [R package] for explo
26504142	python	Pycellerator: an arrow-based reaction-like modelling language for biological simulations.	2016	erator, a [python] library f
26504139	java	IsoMIF Finder: online detection of binding site molecular interaction field similarities.	2016	jsmol (no [java] plugin re
26500152	r	funtooNorm: an R package for normalization of DNA methylation data when there are multiple cell or tissue types.	2016	onorm: an [R package] for norma
26493835	javascript	PDB-Explorer: a web-based interactive map of the protein data bank in shape space.	2015	mented in [javascript] in a plat
26487736	perl	RNA structure framework: automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data.	2016	ritten in [perl] and is fr
26476781	python	A-DaGO-Fun: an adaptable Gene Ontology semantic similarity-based functional analysis tool.	2016	nux using [python] under fre
26476780	java	Scalable clustering algorithms for continuous environmental flow cytometry.	2016	mented in [java] for use w
26471456	python	Computational discovery of specificity-conferring sites in non-ribosomal peptide synthetases.	2016	mented in [python] with flas
26468003	r	BiTrinA--multiscale binarization and trinarization with quality analysis.	2016	ilable on [CRAN].
26458889	c++	A multi-objective optimization approach accurately resolves protein domain architectures.	2016	mented in [C++] and the s
26454281	python	CSSSCL: a python package that uses combined sequence similarity scores for accurate taxonomic classification of long and short sequence reads.	2016	cssscl: a [python] package t
26454280	python	SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data.	2016	mented in [python], and its
26454279	c++	Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic.	2016	mented in [C++]. the sour
26454276	java	Rapid and enhanced remote homology detection by cascading hidden Markov model searches in sequence space.	2016	mented in [java] along wit
26454275	python	miTRATA: a web-based tool for microRNA Truncation and Tailing Analysis.	2016	mented in [python] (version
26454273	python	Jflow: a workflow management system for web applications.	2016	ion and a [python] library p
26454094	python	Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology.	2016	opment of [python] and web-s
26449931	r	CpGFilter: model-based CpG probe filtering with replicates for epigenome-wide association studies.	2016	n via the [R package] 'cpgfilte
26449930	python	HapFlow: visualizing haplotypes in sequencing data.	2016	flow is a [python] applicati
26446136	javascript	The new protein topology graph library web server.	2016	d in php, [javascript], postgres
26446133	mathlab	SIMToolbox: a MATLAB toolbox for structured illumination fluorescence microscopy.	2016	oolbox: a [matlab] toolbox f
26446060	r	Multiple Testing of Gene Sets from Gene Ontology: Possibilities and Pitfalls.	2016	ed in the [R package] cherry.
26445311	r	DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment.	2015	decipher [R package] and sourc
26428291	c++	ALP & FALP: C++ libraries for pairwise local alignment E-values.	2016	p & falp: [C++] libraries
26428289	r	Generalized empirical Bayesian methods for discovery of differential data in high-throughput biology.	2016	ilable on [Bioconductor] http://ww
26428288	c++	Pseudoknots in RNA folding landscapes.	2016	mented in [C++] as standa
26424859	r	Warpgroup: increased precision of metabolomic data processing by consensus integration bound analysis.	2016	en source [R package] available
26424858	r	regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests.	2016	ner is an [R package] that impl
26424855	r	missMethyl: an R package for analyzing data from Illumina's HumanMethylation450 platform.	2016	ethyl: an [R package] for analy
26423836	javascript	Density-based parallel skin lesion border detection with webCL.	2015	ebcl is a [javascript] binding o
26423515	mathlab	Efficient experimental design for uncertainty reduction in gene regulatory networks.	2015	cantly. a [matlab] software
26415849	r	NetBenchmark: a bioconductor package for reproducible benchmarks of gene regulatory network inference.	2015	chmark: a [Bioconductor] package f
26415725	c++	XPIWIT--an XML pipeline wrapper for the Insight Toolkit.	2016	ard-coded [C++] pipelines
26415723	r	ScreenBEAM: a novel meta-analysis algorithm for functional genomics screens via Bayesian hierarchical modeling.	2016	[R package] and sourc
26415722	javascript	Cytoscape.js: a graph theory library for visualisation and analysis.	2016	mented in [javascript]. document
26411870	c++	JBASE: Joint Bayesian Analysis of Subphenotypes and Epistasis.	2016	mented in [C++], supporte
26411869	c++	CLUSTERnGO: a user-defined modelling platform for two-stage clustering of time-series data.	2016	the [C++] and qt so
26411867	r	XLmap: an R package to visualize and score protein structure models based on sites of protein cross-linking.	2016	xlmap: an [R package] to visual
26399714	python	htsint: a Python library for sequencing pipelines that combines data through gene set generation.	2015	htsint: a [python] library f
26384762	c++	Lab Retriever: a software tool for calculating likelihood ratios incorporating a probability of drop-out for forensic DNA profiles.	2015	top of a [C++] implement
26384762	javascript	Lab Retriever: a software tool for calculating likelihood ratios incorporating a probability of drop-out for forensic DNA profiles.	2015	marily in [javascript], on top o
26382197	java	NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles.	2016	mented in [java] with supp
26382193	perl	ICT: isotope correction toolbox.	2016	language [perl] and, ther
26374744	r	mAPKL: R/ Bioconductor package for detecting gene exemplars and revealing their characteristics.	2015	ed in the [R package], which is
26374641	r	A weighting approach for judging the effect of patient strata on high-dimensional risk prediction signatures.	2015	ed in the [R package] coxboost
26369703	python	PyPDB: a Python API for the Protein Data Bank.	2016	pypdb: a [python] api for t
26363176	c++	markophylo: Markov chain analysis on phylogenetic trees.	2016	ritten in [C++] and the i
26363176	r	markophylo: Markov chain analysis on phylogenetic trees.	2016	and fast [R package] is introd
26363029	java	An algorithm for automated layout of process description maps drawn in SBGN.	2016	orithm in [java] is availa
26363028	c++	BamHash: a checksum program for verifying the integrity of sequence data.	2016	mented in [C++], gpl lice
26358728	c++	SeDuS: segmental duplication simulator.	2016	mented in [C++] and can b
26358727	r	Group and sparse group partial least square approaches applied in genomics context.	2016	rehensive [R package] called sg
26342229	r	BMix: probabilistic modeling of occurring substitutions in PAR-CLIP data.	2016	or matlab [and R].
26342229	mathlab	BMix: probabilistic modeling of occurring substitutions in PAR-CLIP data.	2016	lable for [matlab] and r.
26338769	mathlab	Discovering hospital admission patterns using models learnt from electronic hospital records.	2015	full [matlab] source co
26338767	r	DIGGIT: a Bioconductor package to infer genetic variants driving cellular phenotypes.	2015	diggit: a [Bioconductor] package t
26329719	r	CompGO: an R package for comparing and visualizing Gene Ontology enrichment differences between DNA binding experiments.	2015	ompgo: an [R package] for compa
26328606	java	Pan-Tetris: an interactive visualisation for Pan-genomes.	2015	tetris, a [java] based int
26328469	r	VisRseq: R-based visual framework for analysis of sequencing data.	2015	s such as [Bioconductor]. to addre
26323718	c++	NgsRelate: a software tool for estimating pairwise relatedness from next-generation sequencing data.	2015	mented in [C++] and is av
26323716	c	BiopLib and BiopTools--a C programming library and toolset for manipulating protein structure.	2015	ptools--a [C programming] library a
26323713	c++	RASER: reads aligner for SNPs and editing sites of RNA.	2015	ritten in [C++] and freel
26319390	c++	Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis.	2016	mented in [C++] and has b
26319221	c++	BS-SNPer: SNP calling in bisulfite-seq data.	2015	ritten in [C++] and perl,
26319221	perl	BS-SNPer: SNP calling in bisulfite-seq data.	2015	n c++ and [perl], and is f
26315911	r	msa: an R package for multiple sequence alignment.	2015	msa: an [R package] for multi
26315910	python	Identification of hierarchical chromatin domains.	2016	a [python] implement
26315909	c++	glmgraph: an R package for variable selection and predictive modeling of structured genomic data.	2015	in r and [C++] armadillo
26315909	r	glmgraph: an R package for variable selection and predictive modeling of structured genomic data.	2015	graph: an [R package] for varia
26315908	c	HiXCorr: a portable high-speed XCorr engine for high-resolution tandem mass spectrometry.	2015	eloped in [C language]. hence, o
26315907	c++	Fast and accurate approximate inference of transcript expression from RNA-seq data.	2015	in r and [C++], and are
26315907	r	Fast and accurate approximate inference of transcript expression from RNA-seq data.	2015	he bitseq [Bioconductor] package.
26315904	java	LIBRA: LIgand Binding site Recognition Application.	2015	eloped in [java] se 7 with
26315903	perl	Bayexer: an accurate and fast Bayesian demultiplexer for Illumina sequences.	2015	mented in [perl] and freel
26298294	python	Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment.	2015	perl, and [python]. subseque
26298294	perl	Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment.	2015	s like r, [perl], and pyth
26286809	python	svviz: a read viewer for validating structural variants.	2015	mented in [python] and freel
26283514	r	diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data.	2015	iffhic: a [Bioconductor] package t
26283310	r	SIMAT: GC-SIM-MS data analysis tool.	2015	uce a new [R package] called si
26275896	r	DSviaDRM: an R package for estimating disease similarity via dysfunctional regulation mechanism.	2015	iadrm: an [R package] for estim
26272984	r	motifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites.	2015	ed within [Bioconductor].
26261223	java	Vizardous: interactive analysis of microbial populations with single cell resolution.	2015	xecutable [java] archive a
26254488	java	BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements.	2015	ritten in [java]. source c
26249815	r	cgmisc: enhanced genome-wide association analyses and visualization.	2015	gmisc, an [R package] that enab
26249810	python	NRGsuite: a PyMOL plugin to perform docking simulations in real time using FlexAID.	2015	mented in [python] and c/c++
26249809	python	ASSIsT: an automatic SNP scoring tool for in- and outbreeding species.	2015	eloped in [python] and runs
26243017	r	NAM: association studies in multiple populations.	2015	e nam, an [R package] that allo
26231430	r	stringgaussnet: from differentially expressed genes to semantic and Gaussian networks generation.	2015	ssnet, an [R package] that inte
26231427	python	An efficient algorithm for the extraction of HGVS variant descriptions from sequences.	2015	code and [python] interface
26231427	c++	An efficient algorithm for the extraction of HGVS variant descriptions from sequences.	2015	.nl). the [C++] source co
26231426	r	MICC: an R package for identifying chromatin interactions from ChIA-PET data.	2015	micc: an [R package] for ident
26227145	python	BackCLIP: a tool to identify common background presence in PAR-CLIP datasets.	2015	mented in [python]. the comm
26227143	perl	SNPGenie: estimating evolutionary parameters to detect natural selection using pooled next-generation sequencing data.	2015	1.2 is a [perl] program w
26220962	r	MetTailor: dynamic block summary and intensity normalization for robust analysis of mass spectrometry data in metabolomics.	2015	the [R package] mettailor
26220961	r	Designing alternative splicing RNA-seq studies. Beyond generic guidelines.	2015	ge at www.[Bioconductor].org/packa
26209431	r	dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering.	2015	xtend: an [R package] for visua
26208945	python	Object-based representation and analysis of light and electron microscopic volume data using Blender.	2015	embedded [python] applicati
26206305	python	Identifying kinase dependency in cancer cells by integrating high-throughput drug screening and kinase inhibition data.	2015	aded as a [python] function
26206305	mathlab	Identifying kinase dependency in cancer cells by integrating high-throughput drug screening and kinase inhibition data.	2015	tion or a [matlab] script al
26198102	perl	Roary: rapid large-scale prokaryote pan genome analysis.	2015	mented in [perl] and is fr
26187943	r	RxnSim: a tool to compare biochemical reactions.	2015	network, [CRAN] (http://c
26163694	r	SomaticSignatures: inferring mutational signatures from single-nucleotide variants.	2015	the [R package] somaticsi
26163509	r	TiMEx: a waiting time model for mutually exclusive cancer alterations.	2016	conductor [R package] at www.bs
26160651	python	Evaluation of BLAST-based edge-weighting metrics used for homology inference with the Markov Clustering algorithm.	2015	inimalist [python] implement
26153515	java	LayerCake: a tool for the visual comparison of viral deep sequencing data.	2015	ework for [java].
26148744	r	DINGO: differential network analysis in genomics.	2015	[R package] at: odin.
26142188	mathlab	Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems.	2015	nment for [matlab] that pion
26142186	c++	al3c: high-performance software for parameter inference using Approximate Bayesian Computation.	2015	t al3c, a [C++] framework
26130249	python	YBYRÁ facilitates comparison of large phylogenetic trees.	2015	ritten in [python], hence th
26130577	r	A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites.	2015	en-source [R package] at that i
26130576	perl	Estimating beta diversity for under-sampled communities using the variably weighted Odum dissimilarity index and OTUshuff.	2015	a [perl] script fo
26130574	python	ProFET: Feature engineering captures high-level protein functions.	2015	mented in [python] and adapt
26130573	r	Inference of Markovian properties of molecular sequences from NGS data and applications to comparative genomics.	2016	ilable as [R package] 'ngs.mc'
26115986	python	nextflu: real-time tracking of seasonal influenza virus evolution in humans.	2015	[python] and javas
26115986	javascript	nextflu: real-time tracking of seasonal influenza virus evolution in humans.	2015	ython and [javascript] source co
26112292	perl	damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets.	2015	mented in [perl] and is co
26112291	java	Real-time multi-view deconvolution.	2015	olution', [java] wrappers
26112290	r	biRte: Bayesian inference of context-specific regulator activities and transcriptional networks.	2015	ilable on [Bioconductor] (http://b
26099265	c++	Bandage: interactive visualization of de novo genome assemblies.	2015	mented in [C++] and suppo
26099264	r	Sincell: an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq.	2015	e sincell [R package] implement
26093150	javascript	GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications.	2015	ritten in [javascript] using the
26093147	r	An efficient Bayesian inference framework for coalescent-based nonparametric phylodynamics.	2015	nd in the [R package] phylodyn
26092860	r	atSNP: transcription factor binding affinity testing for regulatory SNP detection.	2015	efficient [R package] for ident
26088801	r	Rchemcpp: a web service for structural analoging in ChEMBL, Drugbank and the Connectivity Map.	2015	e and the [R package] are freel
26085504	mathlab	Fast-SL: an efficient algorithm to identify synthetic lethal sets in metabolic networks.	2015	the [matlab] implement
26085503	python	libRoadRunner: a high performance SBML simulation and analysis library.	2015	rough its [python] interface
26085503	c++	libRoadRunner: a high performance SBML simulation and analysis library.	2015	s via its [C++] and c bin
26085503	mathlab	libRoadRunner: a high performance SBML simulation and analysis library.	2015	e apis of [matlab] ( wwwmath
26079347	java	JSBML 1.0: providing a smorgasbord of options to encode systems biology models.	2015	cial pure [java] programmi
26076722	mathlab	REDEMPTION: reduced dimension ensemble modeling and parameter estimation.	2015	through a [matlab] user inte
26072515	mathlab	Inferring orthologous gene regulatory networks using interspecies data fusion.	2015	[matlab] code is a
26072513	c++	Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data.	2015	[C++] and matla
26072513	mathlab	Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data.	2015	c++ and [matlab] code avai
26072511	python	Robust reconstruction of gene expression profiles from reporter gene data using linear inversion.	2015	able as a [python] package (
26072509	python	IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis.	2015	a c++ and [python] program r
26072509	c++	IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis.	2015	able as a [C++] and pytho
26072506	mathlab	Using collective expert judgements to evaluate quality measures of mass spectrometry images.	2015	y and the [matlab] source co
26072499	python	A generic methodological framework for studying single cell motility in high-throughput time-lapse data.	2015	[python] code and
26072472	java	MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphisms.	2015	ritten in [java] and pytho
26072472	python	MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphisms.	2015	java and [python]. it is op
26069263	java	IBS: an illustrator for the presentation and visualization of biological sequences.	2015	mented in [java], while th
26069263	javascript	IBS: an illustrator for the presentation and visualization of biological sequences.	2015	html5 and [javascript]. both the
26063839	r	oposSOM: R-package for high-dimensional portraying of genome-wide expression landscapes on bioconductor.	2015	conductor [R package].
26059717	python	BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.	2015	mented in [python] and datas
26056047	c++	Clotho: addressing the scalability of forward time population genetic simulation.	2015	tion as a [C++] template
26055961	c++	Optimization of sequence alignments according to the number of sequences vs. number of sites trade-off.	2015	en source [C++] implement
26051821	python	Automatising the analysis of stochastic biochemical time-series.	2015	dependent [python] tool to a
26051409	java	adLIMS: a customized open source software that allows bridging clinical and basic molecular research studies.	2015	ritten in [java] j2ee, as
26049161	bash	GeIST: a pipeline for mapping integrated DNA elements.	2015	nation of [bash] shell scr
26049161	perl	GeIST: a pipeline for mapping integrated DNA elements.	2015	pting and [perl]. geist is
26048599	python	Sparse multi-view matrix factorization: a multivariate approach to multiple tissue comparisons.	2015	[python] code is a
26040457	javascript	A web application for the unspecific detection of differentially expressed DNA regions in strand-specific expression data.	2015	n php and [javascript].
26040456	c++	Assembling short reads from jumping libraries with large insert sizes.	2015	mented in [C++] as a part
26034064	r	FourCSeq: analysis of 4C sequencing data.	2015	ed in the [R package] fourcseq
26026169	python	DisVis: quantifying and visualizing accessible interaction space of distance-restrained biomolecular complexes.	2015	disvis, a [python] package a
26026168	r	lpNet: a linear programming approach to reconstruct signal transduction networks.	2015	ach as an [R package] available
26026138	c	QVZ: lossy compression of quality values.	2015	qvz is [written in C] and can b
26026137	c++	ACE: accurate correction of errors using K-mer tries.	2015	mented in [C++] and runs
26026136	r	Differential protein expression and peak selection in mass spectrometry data by binary discriminant analysis.	2015	ed in the [R package] binda, wh
26017500	r	tcR: an R package for T cell receptor repertoire advanced data analysis.	2015	tcr: an [R package] for t cel
26017358	r	MANTIS: an R package that simulates multilocus models of pathogen evolution.	2015	antis: an [R package] that simu
26007226	python	IgSimulator: a versatile immunosequencing simulator.	2015	a c++ and [python] program r
26007226	c++	IgSimulator: a versatile immunosequencing simulator.	2015	able as a [C++] and pytho
26002886	mathlab	Diffusion maps for high-dimensional single-cell analysis of differentiation data.	2015	the [matlab] implement
26002885	r	Bayesian mixture analysis for metagenomic community profiling.	2015	friendly [R package], freely a
26002884	r	tmle.npvi: targeted, integrative search of associations between DNA copy number and gene expression, accounting for DNA methylation.	2015	en-source [R package] tmle.npvi
26002883	r	pwOmics: an R package for pathway-based integration of time-series omics data using public database knowledge.	2015	omics: an [R package] for pathw
25995232	python	When less is more: 'slicing' sequencing data improves read decoding accuracy and de novo assembly quality.	2015	[python] scripts t
25995231	r	ABC: a tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments.	2015	(≥5.18.1) [and R] (≥3.1.1)
25995231	perl	ABC: a tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments.	2015	ritten in [perl] and can b
25991004	r	affy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling.	2015	fy2sv: an [R package] to pre-pr
25987568	python	TRAL: tandem repeat annotation library.	2015	en-source [python] 3 library
25987567	c++	IMSEQ--a fast and error aware approach to immunogenetic sequence analysis.	2015	mented in [C++] using the
25982853	java	ProtDCal: A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins.	2015	ed in the [java] programmi
25980407	python	NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation.	2015	en-source [python] module; b
25979472	r	Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data.	2015	ay offers [Bioconductor] users enh
25972088	r	ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles.	2015	ted as an [R package]. the isop
25971991	r	GENLIB: an R package for the analysis of genealogical data.	2015	enlib: an [R package] for the a
25971742	javascript	GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions.	2015	ichr adds [javascript] code to g
25971741	r	Fast parametric time warping of peak lists.	2015	/ptw) and [CRAN] (http://c
25971740	r	CAPRI: efficient inference of cancer progression models from cross-sectional data.	2015	oncology [R package] and is fr
25968113	python	Domain similarity based orthology detection.	2015	sed using [python] and c++ l
25968113	c++	Domain similarity based orthology detection.	2015	ython and [C++] languages
25964631	r	GOplot: an R package for visually combining expression data with functional analysis.	2015	oplot: an [R package] for visua
25962835	r	A multi-view genomic data simulator.	2015	sses. the [R package] mvbiodata
25957349	r	Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data.	2015	en-source [R package] and appli
25957348	r	INSPEcT: a computational tool to infer mRNA synthesis, processing and degradation dynamics from RNA- and 4sU-seq time course experiments.	2015	ect is an [R package] for the i
25951947	r	Performance of a blockwise approach in variable selection using linkage disequilibrium information.	2015	ed in the [R package] bald (blo
25948716	r	pez: phylogenetics for the environmental sciences.	2015	pez is an [R package] that perm
25943746	r	Estimation of the methylation pattern distribution from deep sequencing data.	2015	in the r [Bioconductor] package m
25943565	r	Controlling false discoveries in high-dimensional situations: boosting with stability selection.	2015	available [R package] stabs (ht
25940563	javascript	Phylesystem: a git-based data store for community-curated phylogenetic estimates.	2015	eployed a [javascript] applicati
25940562	java	HTT-DB: horizontally transferred transposable elements database.	2015	based on [java] and mysql
25933606	python	Pydna: a simulation and documentation tool for DNA assembly strategies using python.	2015	ies using [python].
25931516	c++	'Flatten plus': a recent implementation in WSxM for biological research.	2015	mented in [C++] supported
25928861	r	Moment based gene set tests.	2015	available [Bioconductor] package,
25928765	r	coMET: visualisation of regional epigenome-wide association scan results and DNA co-methylation patterns.	2015	comet, an [R package] and onlin
25926345	r	Polyester: simulating RNA-seq datasets with differential transcript expression.	2015	ter is an [R package] designed
25924931	r	plethy: management of whole body plethysmography data in R.	2015	rt of the [Bioconductor] project h
25924884	c++	UrQt: an efficient software for the Unsupervised Quality trimming of NGS data.	2015	mented in [C++] in an eff
25913208	r	phylogeo: an R package for geographic analysis and visualization of microbiome data.	2015	logeo: an [R package] for geogr
25913205	mathlab	Genome-scale strain designs based on regulatory minimal cut sets.	2015	[matlab] code and
25913204	r	chipPCR: an R package to pre-process raw data of amplification curves.	2015	ippcr: an [R package] to pre-pr
25910694	java	ms-data-core-api: an open-source, metadata-oriented library for computational proteomics.	2015	ritten in [java], enables
25908790	r	MultiMeta: an R package for meta-analyzing multi-phenotype genome-wide association studies.	2015	imeta: an [R package] for meta-
25900919	r	edgeRun: an R package for sensitive, functionally relevant differential expression discovery using an unconditional exact test.	2015	gerun: an [R package] for sensi
25888166	r	micropan: an R-package for microbial pan-genomics.	2015	resent an [R package] for the s
25888118	java	CHEXVIS: a tool for molecular channel extraction and visualization.	2015	th latest [java] plug-in.
25887779	java	OTO: Ontology Term Organizer.	2015	built in [java].
25887573	c++	Automatic segmentation of deep intracerebral electrodes in computed tomography scans.	2015	en source [C++] prototype
25887481	c++	Family-based association analysis: a fast and efficient method of multivariate association analysis with multiple variants.	2015	eloped in [C++] and is av
25886992	r	Pheno2Geno - High-throughput generation of genetic markers and maps from molecular phenotypes for crosses between inbred strains.	2015	e leading [R package] for qtl s
25886979	mathlab	FastMotif: spectral sequence motif discovery.	2015	the [matlab] code of f
25885646	c	FlowClus: efficiently filtering and denoising pyrosequenced amplicons.	2015	s); it is [written in C] and suppo
25884684	c++	histoneHMM: Differential analysis of histone modifications with broad genomic footprints.	2015	ritten in [C++] and compi
25884684	r	histoneHMM: Differential analysis of histone modifications with broad genomic footprints.	2015	led as an [R package]. it runs
25861968	python	MetaSV: an accurate and integrative structural-variant caller for next generation sequencing.	2015	code in [python] is at htt
25847007	r	EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments.	2015	an [R package] containin
25847006	r	Stratifying tumour subtypes based on copy number alteration profiles using next-generation sequence data.	2015	an [R package] to run a
25838463	python	do_x3dna: a tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulations.	2015	ncludes a [python] module dn
25812745	r	KeBABS: an R package for kernel-based analysis of biological sequences.	2015	ebabs: an [R package] for kerne
25805722	python	Identification of cell types from single-cell transcriptomes using a novel clustering method.	2015	atlab and [python]. the sour
25805722	mathlab	Identification of cell types from single-cell transcriptomes using a novel clustering method.	2015	mented in [matlab] and pytho
25792553	r	A robust approach for identifying differentially abundant features in metagenomic samples.	2015	an [R package] for raida
25788625	python	Efficient visualization of high-throughput targeted proteomics experiments: TAPIR.	2015	efficient [python] visualiza
25788622	java	A novel motif-discovery algorithm to identify co-regulatory motifs in large transcription factor and microRNA co-regulatory networks in human.	2015	mented in [java] and avail
25777525	r	Cardinal: an R package for statistical analysis of mass spectrometry-based imaging experiments.	2015	dinal: an [R package] for stati
25765347	r	ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization.	2015	ker is an [R package] for annot
25755273	java	BMRF-Net: a software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method.	2015	mented in [java] and c++,
25755273	c++	BMRF-Net: a software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method.	2015	java and [C++], to ident
25735769	mathlab	Logical transformation of genome-scale metabolic models for gene level applications and analysis.	2015	mented in [matlab], raven to
25725498	c++	L-GRAAL: Lagrangian graphlet-based network aligner.	2015	coded in [C++]. software
25725494	java	GeLL: a generalized likelihood library for phylogenetic models.	2015	t gell, a [java] library t
25725090	r	SimSeq: a nonparametric approach to simulation of RNA-sequence datasets.	2015	ed in the [R package] simseq, w
25717194	c++	Fast, accurate, and reliable molecular docking with QuickVina 2.	2015	the [C++] source co
25717189	r	rSeqNP: a non-parametric approach for detecting differential expression and splicing from RNA-Seq data.	2015	resent an [R package], rseqnp,
25712692	r	specL--an R/Bioconductor package to prepare peptide spectrum matches for use in targeted proteomics.	2015	ed in the [R language] and avail
25707528	c++	PEAT: an intelligent and efficient paired-end sequencing adapter trimming algorithm.	2015	tandalone [C++] source co
25701576	mathlab	Pattern recognition methods to relate time profiles of gene expression with phenotypic data: a comparative study.	2015	the [matlab] code for
25701573	java	Oasis: online analysis of small RNA deep sequencing data.	2015	ython, r, [java], php, c++
25701573	python	Oasis: online analysis of small RNA deep sequencing data.	2015	mented in [python], r, java,
25701573	c++	Oasis: online analysis of small RNA deep sequencing data.	2015	ava, php, [C++] and javas
25701573	javascript	Oasis: online analysis of small RNA deep sequencing data.	2015	, c++ and [javascript]. it is fr
25686638	java	RAPTR-SV: a hybrid method for the detection of structural variants.	2015	ritten in [java] and uses
25677125	r	DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis.	2015	ose is an [R package] providing
25673340	python	MESMER: minimal ensemble solutions to multiple experimental restraints.	2015	, modular [python] plugins e
25667548	c++	A multiobjective memetic algorithm for PPI network alignment.	2015	the [C++] source co
25661541	c++	Whiteboard: a framework for the programmatic visualization of complex biological analyses.	2015	mented in [C++] that enab
25652236	r	BACA: bubble chArt to compare annotations.	2015	le at the [CRAN] repositor
25649621	python	Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets.	2015	cation in [python], availabl
25644271	perl	Transposome: a toolkit for annotation of transposable element families from unassembled sequence reads.	2015	mented in [perl] and is su
25644269	r	ClassifyR: an R package for performance assessment of classification with applications to transcriptomics.	2015	sifyr: an [R package] for perfo
25644268	r	CNOGpro: detection and quantification of CNVs in prokaryotic whole-genome sequencing data.	2015	from the [CRAN] repositor
25638814	mathlab	Factor graph analysis of live cell-imaging data reveals mechanisms of cell fate decisions.	2015	the [matlab] source co
25638808	r	TIMMA-R: an R package for predicting synergistic multi-targeted drug combinations in cancer cell lines or patient-derived samples.	2015	mma-r: an [R package] for predi
25638808	mathlab	TIMMA-R: an R package for predicting synergistic multi-targeted drug combinations in cancer cell lines or patient-derived samples.	2015	original [matlab] code. the
25638391	r	Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data.	2015	ed in the [R package] wavcluste
25637560	python	Omics Pipe: a community-based framework for reproducible multi-omics data analysis.	2015	tandalone [python] package f
25637558	java	Dizzy-Beats: a Bayesian evidence analysis tool for systems biology.	2015	graphical [java] bayesian
25627825	mathlab	SFMetrics: an analysis tool for scanning force microscopy images of biomolecules.	2015	ng within [matlab] environme
25626999	r	Exploring possible DNA structures in real-time polymerase kinetics using Pacific Biosciences sequencer data.	2015	using an [R package] that we h
25626688	c++	MDAT- Aligning multiple domain arrangements.	2015	coded in [C++], and the
25619996	r	protr/ProtrWeb: R package and web server for generating various numerical representation schemes of protein sequences.	2015	protrweb: [R package] and web s
25619995	c++	Bayesian feature selection for high-dimensional linear regression via the Ising approximation with applications to genomics.	2015	he bia in [C++], along wi
25617415	r	ASSIGN: context-specific genomic profiling of multiple heterogeneous biological pathways.	2015	ttp://www.[Bioconductor].org/packa
25609796	r	dslice: an R package for nonparametric testing of associations with application in QTL and gene set analysis.	2015	slice: an [R package] for nonpa
25609794	r	MethylMix: an R package for identifying DNA methylation-driven genes.	2015	ylmix: an [R package] for ident
25600654	mathlab	Sample size calculation in metabolic phenotyping studies.	2015	rithm for [matlab] and gnu o
25592847	r	Semi-supervised adaptive-height snipping of the hierarchical clustering tree.	2015	data sets [and R] code are
25591917	mathlab	Predicting protein functions using incomplete hierarchical labels.	2015	bels. the [matlab] code of p
25591325	javascript	YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia.	2015	nchronous [javascript] and xml (
25568282	c++	A haplotype-based framework for group-wise transmission/disequilibrium tests for rare variant association analysis.	2015	d gtdt in [C++] and the s
25568279	java	GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome.	2015	ebserver, [java] applet, u
25563332	r	Co-expression analysis of high-throughput transcriptome sequencing data with Poisson mixture models.	2015	en-source [R package] htscluste
25550326	r	PRSice: Polygenic Risk Score software.	2015	prsice is [written in R], includin
25550326	bash	PRSice: Polygenic Risk Score software.	2015	ppers for [bash] data mana
25543048	python	An automatic tool to analyze and cluster macromolecular conformations based on self-organizing maps.	2015	nt here a [python] library i
25540184	java	J-Circos: an interactive Circos plotter.	2015	uses the [java] computer
25535243	c++	A Bayesian framework for de novo mutation calling in parents-offspring trios.	2015	the [C++] source co
25527832	c++	Population-based structural variation discovery with Hydra-Multi.	2015	ritten in [C++] and is fr
25524895	java	VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications.	2015	code in [java] and pytho
25524895	python	VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications.	2015	java and [python] along wit
25519981	mathlab	DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis.	2014	reliable [matlab] code for
25505095	python	Epock: rapid analysis of protein pocket dynamics.	2015	rce code, [python] analysis
25505095	c++	Epock: rapid analysis of protein pocket dynamics.	2015	epock [C++] source co
25505094	java	Detection of circular permutations within protein structures using CE-CP.	2015	s part of [biojava] 3 (http:/
25505092	python	NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy.	2015	rsions of [python] and tcl/t
25505090	java	3Dmol.js: molecular visualization with WebGL.	2015	lugins or [java]. 3dmol.js
25505090	javascript	3Dmol.js: molecular visualization with WebGL.	2015	-oriented [javascript] library t
25505087	java	Sputnik: ad hoc distributed computation.	2015	ng only a [java] runtime,
25504849	java	MpTheory Java library: a multi-platform Java library for systems biology based on the Metabolic P theory.	2015	mptheory [java] library:
25504849	r	MpTheory Java library: a multi-platform Java library for systems biology based on the Metabolic P theory.	2015	thematica [and R].
25504849	mathlab	MpTheory Java library: a multi-platform Java library for systems biology based on the Metabolic P theory.	2015	, such as [matlab], gnu octa
25504848	python	repDNA: a Python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequence-order effects.	2015	repdna: a [python] package t
25496126	python	Kiwi: a tool for integration and visualization of network topology and gene-set analysis.	2014	able as a [python] package a
25495450	r	MPAgenomics: an R package for multi-patient analysis of genomic markers.	2014	omics: an [R package] for multi
25494997	perl	Masking as an effective quality control method for next-generation sequencing data analysis.	2014	ield. the [perl] script fo
25492550	r	Identifying and quantifying metabolites by scoring peaks of GC-MS data.	2014	core in a [R package] called me
25491122	python	MCMC implementation of the optimal Bayesian classifier for non-Gaussian models: model-based RNA-Seq classification.	2014	video and [python] source co
25491031	r	Integrating protein structural dynamics and evolutionary analysis with Bio3D.	2014	dependent [R package] under a g
25490956	r	Pathomx: an interactive workflow-based tool for the analysis of metabolomic data.	2014	g matlab® [and R], allowing
25481010	python	SNPlice: variants that modulate Intron retention from RNA-sequencing data.	2015	rs and as [python] source-co
25481009	c++	ICMA: an integrated cardiac modeling and analysis platform.	2015	mented in [C++] using ope
25481008	r	flowCL: ontology-based cell population labelling in flow cytometry.	2015	e through [Bioconductor] (http://w
25480372	r	Semiconductor sequencing: how many flows do you need?	2015	from the [CRAN] repositor
25465054	java	VTBuilder: a tool for the assembly of multi isoform transcriptomes.	2014	mented in [java] and is av
25431350	c	Meta-eQTL: a tool set for flexible eQTL meta-analysis.	2014	ive parts [written in C]. the soft
25431350	r	Meta-eQTL: a tool set for flexible eQTL meta-analysis.	2014	utilities [written in R], with som
25431229	r	An efficient algorithm to explore liquid association on a genome-wide scale.	2014	ttp://www.[Bioconductor].org .
25417205	r	QuasR: quantification and annotation of short reads in R.	2015	grated in [Bioconductor] so that i
25417204	r	Genomation: a toolkit to summarize, annotate and visualize genomic intervals.	2015	built an [R package], genomati
25417203	python	Efficient searching and annotation of metabolic networks using chemical similarity.	2015	[python] files wil
25416747	mathlab	Multilevel regularized regression for simultaneous taxa selection and network construction with metagenomic count data.	2015	e mlrr in [matlab] is availa
25414364	c++	The Victor C++ library for protein representation and advanced manipulation.	2015	he victor [C++] library f
25413436	r	A framework for generalized subspace pattern mining in high-dimensional datasets.	2014	e through [CRAN] (http://c
25398608	python	SNV-PPILP: refined SNV calling for tumor data using perfect phylogenies and ILP.	2015	ritten in [python] and requi
25391397	c++	Optimization method for obtaining nearest-neighbour DNA entropies and enthalpies directly from melting temperatures.	2015	[C++] source co
25388151	java	EVpedia: a community web portal for extracellular vesicles research.	2015	d in php, [java], mysql an
25380959	python	PyFDAP: automated analysis of fluorescence decay after photoconversion (FDAP) experiments.	2015	ritten in [python] and runs
25380958	r	Development of a robust classifier for quality control of reverse-phase protein arrays.	2015	percurve [R package], can be f
25380956	c++	TreeEFM: calculating elementary flux modes using linear optimization in a tree-based algorithm.	2015	mented in [C++] and inter
25378466	r	flowDensity: reproducing manual gating of flow cytometry data by automated density-based cell population identification.	2015	e through [Bioconductor] (http://m
25371478	java	JAMSS: proteomics mass spectrometry simulation in Java.	2015	lation in [java].
25371114	r	Optimising parallel R correlation matrix calculations on gene expression data using MapReduce.	2014	ed on the [R package] rhipe, de
25371041	r	Missing value imputation in high-dimensional phenomic data: imputable or not, and how?	2014	thods. an [R package] phenomei
25367050	mathlab	A MATLAB tool for pathway enrichment using a topology-based pathway regulation score.	2014	a [matlab] tool for
25362092	c++	Mass spectrometry-based protein identification with accurate statistical significance assignment.	2015	mented in [C++] on a linu
25359893	mathlab	eQTL epistasis: detecting epistatic effects and inferring hierarchical relationships of genes in biological pathways.	2015	the [matlab] source co
25359149	java	CIG-P: Circular Interaction Graph for Proteomics.	2014	through a [java] based gui
25355790	r	Detecting time periods of differential gene expression using Gaussian processes: an application to endothelial cells exposed to radiotherapy dose fraction.	2015	[R package] 'nsgp' is
25348213	python	DIANA--algorithmic improvements for analysis of data-independent acquisition MS data.	2015	scala and [python] and avail
25344501	c	iDoComp: a compression scheme for assembled genomes.	2015	docomp is [written in C] and can b
25344498	c++	Using 2k + 2 bubble searches to find single nucleotide polymorphisms in k-mer graphs.	2015	ode for a [C++] implement
25344497	javascript	Semantic Body Browser: graphical exploration of an organism and spatially resolved expression data visualization.	2015	wser is a [javascript] web appli
25344496	java	MP-GeneticSynth: inferring biological network regulations from time series.	2015	ynth is a [java] tool for
25342065	python	piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing.	2015	ash, c++, [python], perl and
25342065	c++	piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing.	2015	in bash, [C++], python,
25342065	r	piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing.	2015	hon, perl [and R]. pipipes
25342065	bash	piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing.	2015	mented in [bash], c++, pyt
25342065	perl	piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing.	2015	, python, [perl] and r. pi
25338717	python	FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data.	2015	licensed [python] 2.7 code
25336502	perl	Simple, rapid and accurate genotyping-by-sequencing from aligned whole genomes with ArrayMaker.	2015	mented in [perl] and runs
25336500	r	Statistical significance of variables driving systematic variation in high-dimensional data.	2015	ilable in [CRAN].
25332377	r	Seed: a user-friendly tool for exploring and visualizing microbial community data.	2015	. seed is [written in R] using the
25331652	perl	SummonChimera infers integrated viral genomes with nucleotide precision from NGS data.	2014	mera is a [perl] program t
25322836	python	Rcount: simple and flexible RNA-Seq read counting.	2015	s, useful [python] and r scr
25322836	c++	Rcount: simple and flexible RNA-Seq read counting.	2015	mented in [C++] using the
25322836	r	Rcount: simple and flexible RNA-Seq read counting.	2015	ul python [and R] scripts a
25322835	java	miRseqViewer: multi-panel visualization of sequence, structure and expression for analysis of microRNA sequencing data.	2015	mented in [java], is avail
25319962	mathlab	GeneNet Toolbox for MATLAB: a flexible platform for the analysis of gene connectivity in biological networks.	2015	olbox for [matlab] (also ava
25301849	java	NOVA: a software to analyze complexome profiling data.	2015	at least [java] 7 and run
25286921	r	Chimera: a Bioconductor package for secondary analysis of fusion products.	2014	himera: a [Bioconductor] package f
25286920	r	Deviance residuals-based sparse PLS and sparse kernel PLS regression for censored data.	2015	le on the [CRAN] and is ma
25273112	java	MulRF: a software package for phylogenetic analysis using multi-copy gene trees.	2015	he gui in [java] swing.
25273112	c++	MulRF: a software package for phylogenetic analysis using multi-copy gene trees.	2015	mented in [C++] and the g
25273109	java	KDDN: an open-source Cytoscape app for constructing differential dependency networks with significant rewiring.	2015	nted as a [java] cytoscape
25273108	mathlab	Inference of protein kinetics by stochastic modeling and simulation of fluorescence recovery after photobleaching experiments.	2015	mented in [matlab] r2011b. m
25273107	perl	ExportAid: database of RNA elements regulating nuclear RNA export in mammals.	2015	mented in [perl], mysql, a
25273107	javascript	ExportAid: database of RNA elements regulating nuclear RNA export in mammals.	2015	pache and [javascript] with all
25273104	r	WhopGenome: high-speed access to whole-genome variation and sequence data in R.	2015	hopgenome [R package] is availa
25273102	python	A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature.	2015	a [python] package f
25267467	r	DupChecker: a bioconductor package for checking high-throughput genomic data redundancy in meta-analysis.	2014	hecker: a [Bioconductor] package f
25266225	python	GLAD: a mixed-membership model for heterogeneous tumor subtype classification.	2015	a [python] module im
25266224	c++	Sigma: strain-level inference of genomes from metagenomic analysis for biosurveillance.	2015	mented in [C++] with sour
25265915	python	Polyphony: superposition independent methods for ensemble-based drug discovery.	2014	oded in a [python] package c
25262154	r	Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking.	2015	ly in the [R language]. it can b
25262153	r	switchBox: an R package for k-Top Scoring Pairs classifier development.	2015	chbox: an [R package] for k-top
25260700	python	HTSeq--a Python framework to work with high-throughput sequencing data.	2015	htseq--a [python] framework
25260699	r	EasyStrata: evaluation and visualization of stratified genome-wide association meta-analysis data.	2015	the [R package] easystrat
25260628	r	DiscML: an R package for estimating evolutionary rates of discrete characters using maximum likelihood.	2014	iscml: an [R package] for estim
25252999	c++	Ensemble analysis of adaptive compressed genome sequencing strategies.	2014	mbler 2.0 [C++] source co
25246431	mathlab	NAIL, a software toolset for inferring, analyzing and visualizing regulatory networks.	2015	mented in [matlab], runs on
25246429	r	Rcpi: R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions.	2015	from the [Bioconductor] site (htt
25236458	r	Using population data for assessing next-generation sequencing performance.	2015	sing perl [and R] can be fo
25236458	perl	Using population data for assessing next-generation sequencing performance.	2015	ion using [perl] and r can
25212756	r	UNDO: a Bioconductor R package for unsupervised deconvolution of mixed gene expressions in tumor samples.	2015	conductor [R package] for unsup
25212755	java	cddApp: a Cytoscape app for accessing the NCBI conserved domain database.	2015	ritten in [java] and freel
25202135	r	Performance evaluation of DNA copy number segmentation methods.	2015	-platform [R package] jointseg,
25192743	r	Snowball: resampling combined with distance-based regression to discover transcriptional consequences of a driver mutation.	2015	[R package] and sourc
25192741	python	BalestraWeb: efficient online evaluation of drug-target interactions.	2015	ted using [python], flask, n
25189781	r	subSeq: determining appropriate sequencing depth through efficient read subsampling.	2014	he subseq [R package], which us
25176396	javascript	jvenn: an interactive Venn diagram viewer.	2014	is a new [javascript] library.
25173419	r	poRe: an R package for the visualization and analysis of nanopore sequencing data.	2015	pore: an [R package] for the v
25165095	c++	LoRDEC: accurate and efficient long read error correction.	2014	ritten in [C++], tested o
25165094	perl	MIRPIPE: quantification of microRNAs in niche model organisms.	2014	mented in [perl] and integ
25165093	perl	MR_predictor: a simulation engine for Mendelian Randomization studies.	2014	mented in [perl], and the
25161255	r	Fast randomization of large genomic datasets while preserving alteration counts.	2014	loped the [R package] birewire,
25161251	python	Large-scale automated identification of mouse brain cells in confocal light sheet microscopy images.	2014	mented in [python] and makes
25161247	mathlab	Drug susceptibility prediction against a panel of drugs using kernelized Bayesian multitask learning.	2014	our [matlab] implement
25161243	c++	RidgeRace: ridge regression for continuous ancestral character estimation on phylogenetic trees.	2014	mented in [C++] as a stan
25161242	c++	Polytomy refinement for the correction of dubious duplications in gene trees.	2014	the [C++] source co
25161235	mathlab	Causal network inference using biochemical kinetics.	2014	[matlab] r2014a so
25161225	r	Broad-Enrich: functional interpretation of large sets of broad genomic regions.	2014	rsion and [R package].
25161224	r	Two-dimensional segmentation for analyzing Hi-C data.	2014	he hicseg [R package] is availa
25161219	c++	Lambda: the local aligner for massive biological data.	2014	en-source [C++] library f
25158845	perl	APTE: identification of indirect read-out A-DNA promoter elements in genomes.	2014	a [perl] program (
25152233	perl	ExpTreeDB: web-based query and visualization of manually annotated gene expression profiling experiments of human and mouse from GEO.	2014	mented in [perl], php, r,
25150250	python	ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments.	2014	mented in [python] 2.7, usin
25150247	c++	Cosi2: an efficient simulator of exact and approximate coalescent with selection.	2014	a free [C++] implement
25147360	javascript	Visualization of protein sequence features using JavaScript and SVG with pViz.js.	2014	res using [javascript] and svg w
25147359	python	PyBamView: a browser-based application for viewing short read alignments.	2014	standard [python] package.
25147358	r	MethylAid: visual and interactive quality control of large Illumina 450k datasets.	2014	kage (www.[Bioconductor].org/packa
25143291	python	Poretools: a toolkit for analyzing nanopore sequence data.	2014	ritten in [python] as both a
25123905	python	SCDFinder, a web-based tool for the identification of putative novel ATM and ATR targets.	2014	pearl and [python], and is a
25123902	c++	Cross-validation under separate sampling: strong bias and how to correct it.	2014	e code in [C++], along wi
25123900	python	READemption-a tool for the computational analysis of deep-sequencing-based transcriptome data.	2014	mented in [python] and is pu
25123899	r	NetComm: a network analysis tool based on communicability.	2014	hod as an [R package] for use i
25115706	python	Figmop: a profile HMM to identify genes and bypass troublesome gene models in draft genomes.	2014	in c and [python] and is su
25100686	c++	MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers.	2014	ritten in [C++] with open
25095879	python	Tracking global changes induced in the CD4 T-cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence.	2014	in r and [python], and sour
25086004	r	Bias correction for selecting the minimal-error classifier from many machine learning models.	2014	uracy. an [R package] 'mlbias'
25078398	r	Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data.	2014	ttp://www.[Bioconductor].org/. a v
25077818	java	Towards a HPC-oriented parallel implementation of a learning algorithm for bioinformatics applications.	2014	n for the [java] programmi
25075120	r	NetPathMiner: R/Bioconductor package for network path mining through gene expression.	2014	e through [Bioconductor] and from
25075118	c++	FARVAT: a family-based rare variant association test.	2014	mented in [C++], and appl
25075116	c++	Trowel: a fast and accurate error correction module for Illumina sequencing reads.	2014	ritten in [C++] and is pr
25075114	r	Metabomxtr: an R package for mixture-model analysis of non-targeted metabolomics data.	2014	omxtr: an [R package] for mixtu
25075113	perl	Circleator: flexible circular visualization of genome-associated data with BioPerl and SVG.	2014	ator is a [perl] applicati
25066046	mathlab	Hamiltonian Monte Carlo methods for efficient parameter estimation in steady state dynamical systems.	2014	ases. the [matlab] sources i
25064568	perl	e-Driver: a novel method to identify protein regions driving cancer.	2014	a [perl] script wi
25064564	c++	Compression and fast retrieval of SNP data.	2014	nted in a [C++] library,
25061071	r	FisHiCal: an R package for iterative FISH-based calibration of Hi-C data.	2014	hical: an [R package] for itera
25061070	python	STAMP: statistical analysis of taxonomic and functional profiles.	2014	gnu gpl. [python] source co
25061069	mathlab	Inferring condition-specific miRNA activity from matched miRNA and mRNA expression data.	2014	the r and [matlab] scripts a
25061068	r	Más-o-menos: a simple sign averaging method for discrimination in genomic data analysis.	2014	mitted to [Bioconductor].
25053745	r	sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments.	2014	nted as a [Bioconductor] package i
25035399	r	lrgpr: interactive linear mixed model analysis of genome-wide association studies with composite hypothesis testing and regression diagnostics in R.	2014	stry. our [R package], lrgpr, a
25028724	r	AffyPipe: an open-source pipeline for Affymetrix Axiom genotyping workflow.	2014	s) and an [R package] (snpolish
25012182	r	repfdr: a tool for replicability analysis for genome-wide association studies.	2014	the [R package] repfdr pr
25005023	perl	Simulate_PCR for amplicon prediction and annotation from multiplex, degenerate primers and probes.	2014	mand line [perl] script fr
25004928	r	A test for comparing two groups of samples when analyzing multiple omics profiles.	2014	rt of the [Bioconductor] package s
24994891	mathlab	FindPath: a Matlab solution for in silico design of synthetic metabolic pathways.	2014	ndpath: a [matlab] solution
24990767	r	A spatial simulation approach to account for protein structure when identifying non-random somatic mutations.	2014	alk. the [R package] is availa
24990606	r	Intensity drift removal in LC/MS metabolomics by common variance compensation.	2014	le as the [R package] intcor at
24990605	java	ARBitrator: a software pipeline for on-demand retrieval of auto-curated nifH sequences from GenBank.	2014	[java] source an
24990604	r	RAPIDR: an analysis package for non-invasive prenatal testing of aneuploidy.	2014	en-source [R package] that impl
24990603	c++	GATB: Genome Assembly & Analysis Tool Box.	2014	ritten in [C++] and is av
24982428	python	COSMOS: Python library for massively parallel workflows.	2014	cosmos: [python] library f
24974206	r	bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS).	2014	s/. it is [using R] (http://w
24974204	python	Learning protein-DNA interaction landscapes by integrating experimental data through computational models.	2014	mpete and [python] source co
24966365	bash	H3M2: detection of runs of homozygosity from whole-exome sequencing data.	2014	ection of [bash], r and fo
24966365	fortran	H3M2: detection of runs of homozygosity from whole-exome sequencing data.	2014	sh, r and [fortran] scripts a
24965054	mathlab	Ycasd - a tool for capturing and scaling data from graphical representations.	2014	tted as a [matlab] or an r m
24947750	c++	Omega: an overlap-graph de novo assembler for metagenomics.	2014	mented in [C++] with sour
24939150	python	DAFGA: diversity analysis of functional gene amplicons.	2014	veloped a [python] script pa
24938393	r	CIRCUS: a package for Circos display of structural genome variations from paired-end and mate-pair sequencing data.	2014	mented an [R package] called ci
24938393	perl	CIRCUS: a package for Circos display of structural genome variations from paired-end and mate-pair sequencing data.	2014	2009), a [perl] script, i
24932009	python	Pareto-optimal phylogenetic tree reconciliation.	2014	our [python] tools are
24932008	python	A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data.	2014	[python] and matla
24932008	mathlab	A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data.	2014	ython and [matlab] implement
24931999	java	Stochastic EM-based TFBS motif discovery with MITSU.	2014	[java] executabl
24931992	python	A statistical approach for inferring the 3D structure of the genome.	2014	a [python] implement
24931977	c++	Graph-regularized dual Lasso for robust eQTL mapping.	2014	for both [C++] version a
24931977	mathlab	Graph-regularized dual Lasso for robust eQTL mapping.	2014	rsion and [matlab] version i
24931973	r	Cross-study validation for the assessment of prediction algorithms.	2014	e through [Bioconductor].
24930143	mathlab	LICRE: unsupervised feature correlation reduction for lipidomics.	2014	the [matlab] implement
24930138	java	The Scramble conversion tool.	2014	ion is in [java]. we prese
24930009	r	Determination of sample size for a multi-class classifier based on single-nucleotide polymorphisms: a volume under the surface approach.	2014	anual for [R package] samplesi
24929920	perl	An integrative method to normalize RNA-Seq data.	2014	ritten in [perl] and avail
24928209	r	NetBioV: an R package for visualizing large network data in biology and medicine.	2014	tbiov: an [R package] for visua
24925766	python	L.U.St: a tool for approximated maximum likelihood supertree reconstruction.	2014	ackage, a [python] tool for
24915860	mathlab	Spot quantification in two dimensional gel electrophoresis image analysis: comparison of different approaches and presentation of a novel compound fitting algorithm.	2014	ripted in [matlab] (mathwork
24913447	c++	SMARTPOP: inferring the impact of social dynamics on genetic diversity through high speed simulations.	2014	coded in [C++] and is he
24909518	java	MiningABs: mining associated biomarkers across multi-connected gene expression datasets.	2014	reatment. [java] source co
24907369	java	ABRA: improved coding indel detection via assembly-based realignment.	2014	nation of [java] and c/c++
24907368	r	Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction.	2014	performed [using R] version 2
24907367	r	MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure.	2014	hp), perl [and R]. it is fr
24907367	perl	MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure.	2014	or (php), [perl] and r. it
24907367	javascript	MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure.	2014	e node.js [javascript] framework
24906803	c++	hsphase: an R package for pedigree reconstruction, detection of recombination events, phasing and imputation of half-sib family groups.	2014	mented in [C++] and paral
24906803	r	hsphase: an R package for pedigree reconstruction, detection of recombination events, phasing and imputation of half-sib family groups.	2014	phase: an [R package] for pedig
24903420	r	Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures.	2014	ushi) and [Bioconductor] (http://b
24903419	r	Gene set analysis: limitations in popular existing methods and proposed improvements.	2014	ilable as [R package] from cran
24894503	r	Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series.	2014	pro is an [R package] specifica
24886250	r	KRLMM: an adaptive genotype calling method for common and low frequency variants.	2014	d via the [Bioconductor] project (
24886202	r	An R package that automatically collects and archives details for reproducible computing.	2014	an [R package] that auto
24885957	python	MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.	2014	ilable in [python] via a wra
24885957	r	MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.	2014	uded. the [R package] has been
24885957	mathlab	MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.	2014	an r and [matlab] optimizat
24885091	java	BLASTGrabber: a bioinformatic tool for visualization, analysis and sequence selection of massive BLAST data.	2014	nted as a [java] applicati
24884810	python	GO2MSIG, an automated GO based multi-species gene set generator for gene set enrichment analysis.	2014	erl, r or [python]. the outp
24884810	perl	GO2MSIG, an automated GO based multi-species gene set generator for gene set enrichment analysis.	2014	s such as [perl], r or pyt
24876377	r	PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data.	2014	cnv/, and [R package] at https:
24876377	perl	PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data.	2014	ted using [perl] and r, an
24876375	java	CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures.	2014	ritten in [java]. binaries
24872424	java	CODOC: efficient access, analysis and compression of depth of coverage signals.	2014	[java] source co
24867942	c++	keeSeek: searching distant non-existing words in genomes for PCR-based applications.	2014	mented in [C++] and cuda
24867941	python	MIPgen: optimized modeling and design of molecular inversion probes for targeted resequencing.	2014	ompanying [python] scripts a
24867941	c++	MIPgen: optimized modeling and design of molecular inversion probes for targeted resequencing.	2014	mented in [C++]. source c
24860160	perl	Identification of chromosomal translocation hotspots via scan statistics.	2014	in r and [perl]. source c
24860159	java	GenomeVISTA--an integrated software package for whole-genome alignment and visualization.	2014	c/c++ and [java], the sour
24860159	perl	GenomeVISTA--an integrated software package for whole-genome alignment and visualization.	2014	mented in [perl], c/c++ an
24849580	mathlab	Accurate cell segmentation in microscopy images using membrane patterns.	2014	[matlab] code and
24849579	c++	MaxLink: network-based prioritization of genes tightly linked to a disease seed set.	2014	tation in [C++], and the
24836530	r	MethylSig: a whole genome DNA methylation analysis pipeline.	2014	ble as an [R package] at http:/
24833804	c++	Memory-efficient RNA energy landscape exploration.	2014	rt of the [C++] energy la
24828656	c++	Kmacs: the k-mismatch average common substring approach to alignment-free sequence comparison.	2014	mented in [C++], and the
24825614	java	PLAAC: a web and command-line application to identify proteins with prion-like amino acid composition.	2014	mented in [java], with vis
24825612	python	PyCorrFit-generic data evaluation for fluorescence correlation spectroscopy.	2014	the [python] source co
24813215	r	compcodeR--an R package for benchmarking differential expression methods for RNA-seq data.	2014	coder--an [R package] for bench
24813214	r	Efficient RNA isoform identification and quantification from RNA-Seq data with network flows.	2014	ble as an [R package] from the
24812342	mathlab	PhenoNet: identification of key networks associated with disease phenotype.	2014	[matlab] code is a
24812338	r	RNASeqGUI: a GUI for analysing RNA-Seq data.	2014	rnaseqgui [R package], a graphi
24812337	mathlab	SEK: sparsity exploiting k-mer-based estimation of bacterial community composition.	2014	dependent [matlab] implement
24794933	r	unifiedWMWqPCR: the unified Wilcoxon-Mann-Whitney test for analyzing RT-qPCR data in R.	2014	veloped a [Bioconductor] package f
24794931	r	MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments.	2014	stats: an [R package] for stati
24794927	c++	A fast and powerful tree-based association test for detecting complex joint effects in case-control studies.	2014	mented in [C++] and r and
24794927	r	A fast and powerful tree-based association test for detecting complex joint effects in case-control studies.	2014	ed in c++ [and R] and suppo
24778109	fortran	Regulatory interactions maintaining self-renewal of human embryonic stem cells as revealed through a systems analysis of PI3K/AKT pathway.	2014	[fortran] codes for
24771560	java	WebProtégé: a collaborative Web-based platform for editing biomedical ontologies.	2014	mented in [java] and javas
24771560	javascript	WebProtégé: a collaborative Web-based platform for editing biomedical ontologies.	2014	java and [javascript] using the
24764462	r	On non-detects in qPCR data.	2014	ed in the [R package], nondetec
24764461	python	relax: the analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data.	2014	ritten in [python] with c mo
24764459	r	kdetrees: Non-parametric estimation of phylogenetic tree distributions.	2014	ed as the [R package] kdetrees
24755303	r	A power set-based statistical selection procedure to locate susceptible rare variants associated with complex traits with sequencing data.	2014	an [R package] 'rvsel' c
24753490	r	Rgb: a scriptable genome browser for R.	2014	data, no [R package] currently
24753486	r	aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data.	2014	alfq is [written in R] and freel
24747219	python	DSRC 2--Industry-oriented compression of FASTQ files.	2014	or, c and [python] libraries
24740360	r	Inferring rare disease risk variants based on exact probabilities of sharing by multiple affected relatives.	2014	es of the [R package] rvsharing
24733291	r	R PheWAS: data analysis and plotting tools for phenome-wide association studies in the R environment.	2014	this [R package] is freely
24728858	java	A change-point model for identifying 3'UTR switching by next-generation RNA sequencing.	2014	mented in [java] and can b
24728855	r	geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees.	2014	e popular [R package] geiger. w
24728852	mathlab	Direct calculation of elementary flux modes satisfying several biological constraints in genome-scale metabolic networks.	2014	[matlab] code is p
24675730	r	CAGExploreR: an R package for the analysis and visualization of promoter dynamics across multiple experiments.	2014	lorer: an [R package] for the a
24403538	python	Allerdictor: fast allergen prediction using text classification techniques.	2014	mented in [python] and avail
24395754	r	QCGWAS: A flexible R package for automated quality control of genome-wide association results.	2014	flexible [R package] for autom
24389661	r	AbsCN-seq: a statistical method to estimate tumor purity, ploidy and absolute copy numbers from next-generation sequencing data.	2014	the [R package] abscnseq
24389660	c	Estimation of fluorescence-tagged RNA numbers from spot intensities.	2014	xtensions [written in C] for param
24389660	mathlab	Estimation of fluorescence-tagged RNA numbers from spot intensities.	2014	[matlab] extension
24389657	python	Bias from removing read duplication in ultra-deep sequencing experiments.	2014	a [python] implement
24371153	r	SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes.	2014	nted in c [and R] and are p
24712852	java	TOPS: a versatile software tool for statistical analysis and visualization of combinatorial gene-gene and gene-drug interaction screens.	2014	lysis), a [java] and r-bas
24711652	python	Filling annotation gaps in yeast genomes using genome-wide contact maps.	2014	with the [python] code and
24700319	r	rTANDEM, an R/Bioconductor package for MS/MS protein identification.	2014	ssociated [R package], shinytan
24695406	python	Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity.	2014	ritten in [python] and is pu
24681909	r	flowFit: a Bioconductor package to estimate proliferation in cell-tracking dye studies.	2014	lowfit: a [Bioconductor] package t
24681908	c++	molBLOCKS: decomposing small molecule sets and uncovering enriched fragments.	2014	le as gpl [C++] source co
24681907	r	VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants.	2014	tation: a [Bioconductor] package f
24681904	r	CorMut: an R/Bioconductor package for computing correlated mutations based on selection pressure.	2014	mut is an [R package] designed
24681903	java	Census 2: isobaric labeling data analysis.	2014	requires [java] version 6
24678608	r	Differential meta-analysis of RNA-seq data from multiple studies.	2014	fects. an [R package] metarnase
24669769	r	A graph theoretic approach to utilizing protein structure to identify non-random somatic mutations.	2014	hods. the [R package] is availa
24669753	python	FreeContact: fast and free software for protein contact prediction from residue co-evolution.	2014	perl and [python] modules.
24669753	c++	FreeContact: fast and free software for protein contact prediction from residue co-evolution.	2014	the free [C++] library
24669753	perl	FreeContact: fast and free software for protein contact prediction from residue co-evolution.	2014	s well as [perl] and pytho
24659106	c++	Improved transcript isoform discovery using ORF graphs.	2014	ilable as [C++] source co
24659105	r	massiR: a method for predicting the sex of samples in gene expression microarray datasets.	2014	nted as a [Bioconductor] package i
24659032	r	TroX: a new method to learn about the genesis of aneuploidy from trisomic products of conception.	2014	an [R package] implement
24655717	r	spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.	2014	licer: an [R package] for class
24651968	python	tqDist: a library for computing the quartet and triplet distances between binary or general trees.	2014	er with a [python] module an
24651968	r	tqDist: a library for computing the quartet and triplet distances between binary or general trees.	2014	le and an [R package] for scrip
24650281	python	The characteristic direction: a geometrical approach to identify differentially expressed genes.	2014	uages: r, [python], matlab a
24650281	mathlab	The characteristic direction: a geometrical approach to identify differentially expressed genes.	2014	, python, [matlab] and mathe
24648041	c++	Basin Hopping Graph: a computational framework to characterize RNA folding landscapes.	2014	mented in [C++] as standa
24646301	perl	ShatterProof: operational detection and quantification of chromothripsis.	2014	://search.[CPAN].org/~sgov
24642064	java	KAnalyze: a fast versatile pipelined k-mer toolkit.	2014	mented in [java] 7, and th
24642064	perl	KAnalyze: a fast versatile pipelined k-mer toolkit.	2014	built on [perl] and linux
24642063	perl	Prokka: rapid prokaryotic genome annotation.	2014	mented in [perl] and is fr
24642062	mathlab	Piecewise-constant and low-rank approximation for identification of recurrent copy number variations.	2014	the [matlab] code is a
24642061	r	An R package to analyse LC/MS metabolomic data: MAIT (Metabolite Automatic Identification Toolkit).	2014	an [R package] to analys
24632499	mathlab	A general method for accurate estimation of false discovery rates in identification of differentially expressed genes.	2014	mented in [matlab] and is av
24632498	perl	FSuite: exploiting inbreeding in dense SNP chip and exome data.	2014	eloped in [perl] and uses
24618474	mathlab	Characterization of p38 MAPK isoforms for drug resistance study using systems biology approach.	2014	data and [matlab] source co
24618468	r	Genome-wide quantitative analysis of DNA methylation from bisulfite sequencing data.	2014	s part of [Bioconductor] at www.bi
24618465	java	A personalized committee classification approach to improving prediction of breast cancer metastasis.	2014	atlab and [java] available
24618465	mathlab	A personalized committee classification approach to improving prediction of breast cancer metastasis.	2014	mented in [matlab] and java
24618464	java	The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation.	2014	mented in [java] and makes
24618464	perl	The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation.	2014	java and [perl]. the tool
24618463	java	A gradient-boosting approach for filtering de novo mutations in parent-offspring trios.	2014	nation of [java] and r is
24618463	r	A gradient-boosting approach for filtering de novo mutations in parent-offspring trios.	2014	n of java [and R] is freely
24618462	perl	The Bio-Community Perl toolkit for microbial ecology.	2014	community [perl] toolkit f
24603986	r	Estimating optimal window size for analysis of low-coverage next-generation sequence data.	2014	an [R package] to estima
24603985	python	PyRAD: assembly of de novo RADseq loci for phylogenetic analyses.	2014	ritten in [python] and freel
24590441	mathlab	Protein fold recognition using geometric kernel data fusion.	2014	the [matlab] code used
24585771	python	Wrangling Galaxy's reference data.	2014	mented in [python] and has b
24578404	perl	Accurate computational prediction of the transcribed strand of CRISPR non-coding RNAs.	2014	the [perl] source co
24574115	java	BioPlat: a software for human cancer biomarker discovery.	2014	mented in [java] and suppo
24567545	c++	iCall: a genotype-calling algorithm for rare, low-frequency and common variants on the Illumina exome array.	2014	mented in [C++] for use o
24567544	javascript	jHeatmap: an interactive heatmap viewer for the web.	2014	adaptable [javascript] library d
24564732	r	The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again.	2014	ilable in [Bioconductor] for subse
24564706	python	Finishing bacterial genome assemblies with Mix.	2013	mented in [python] and is av
24564704	java	Random forests on Hadoop for genome-wide association studies of multivariate neuroimaging phenotypes.	2013	the [java] codes are
24564437	mathlab	HCS-Neurons: identifying phenotypic changes in multi-neuron images upon drug treatments of high-content screening.	2013	nloadable [matlab] project a
24564336	mathlab	ProphNet: a generic prioritization method through propagation of information.	2014	ophnet. a [matlab] implement
24564231	r	Efficient digest of high-throughput sequencing data in a reproducible report.	2013	uses the [R language] and bioco
24558116	c	MRHMMs: multivariate regression hidden Markov models and the variantS.	2014	ftware is [written in C] for the s
24555693	r	Statistical hypothesis testing of factor loading in principal component analysis and its application to metabolite set enrichment analysis.	2014	eloped an [R package] mseapca
24554630	mathlab	Automated analysis of giant unilamellar vesicles using circular Hough transformation.	2014	mented in [matlab] (the math
24535097	r	SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data integrating differential expression and splicing.	2014	eqgsea: a [Bioconductor] package f
24532724	r	ADaCGH2: parallelized analysis of (big) CNA data.	2014	gh2 is an [R package] available
24532722	c++	fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data.	2014	ritten in [C++] using ope
24532720	r	LPmerge: an R package for merging genetic maps by linear programming.	2014	merge: an [R package] for mergi
24532718	python	TSSV: a tool for characterization of complex allelic variants in pure and mixed genomes.	2014	tssv as a [python] package t
24519380	r	An efficient algorithm for accurate computation of the Dirichlet-multinomial log-likelihood function.	2014	r work an [R package] giving ac
24511080	python	HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization.	2014	mented in [python], and sour
24501098	r	Visualization and probability-based scoring of structural variants within repetitive sequences.	2014	hod as an [R package] available
24499370	r	Mining locus tags in PubMed Central to improve microbial gene annotation.	2014	eloped an [R package] called pm
24499321	c++	Improving read mapping using additional prefix grams.	2014	mented in [C++], and the
24497503	python	AMASS: a database for investigating protein structures.	2014	nted with [biopython] and apach
24493035	perl	ARTS: automated randomization of multiple traits for study design.	2014	mented in [perl] and is av
24489371	c++	StochHMM: a flexible hidden Markov model tool and C++ library.	2014	tool and [C++] library.
24489369	r	Comparing DNA integration site clusters with scan statistics.	2014	rxcluster [R package] containin
24489367	mathlab	Bayesian joint analysis of heterogeneous genomics data.	2014	ritten in [matlab] and has b
24478339	r	Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays.	2014	rehensive [Bioconductor] package f
24470576	bash	NGSANE: a lightweight production informatics framework for high-throughput data analysis.	2014	rom linux [bash] commands
24470574	python	PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations.	2014	mented in [python] and c++.
24470574	c++	PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations.	2014	ython and [C++]. it bundl
24458951	r	The most informative spacing test effectively discovers biologically relevant outliers or multiple modes in expression.	2014	the oasis [R package] at http:/
24451629	r	h5vc: scalable nucleotide tallies with HDF5.	2014	rough the [Bioconductor] project.
24451624	r	CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data.	2014	cafe: an [R package] for the d
24451622	r	Reference-free cell mixture adjustments in analysis of DNA methylation data.	2014	le in the [R package] reffreeew
24447369	mathlab	Gene expression and nucleotide composition are associated with genic methylation level in Oryza sativa.	2014	he genes. [matlab] code with
24444459	java	BioShell-Threading: versatile Monte Carlo package for protein 3D threading.	2014	a set of [java] classes c
24443383	r	ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics.	2014	metab: an [R package] for bayes
24428888	r	OncomiRdbB: a comprehensive database of microRNAs and their targets in breast cancer.	2014	using the ['R'] algorithm
24423115	python	kruX: matrix-based non-parametric eQTL discovery.	2014	n matlab, [python] and r tha
24423115	r	kruX: matrix-based non-parametric eQTL discovery.	2014	b, python [and R] that uses
24423115	mathlab	kruX: matrix-based non-parametric eQTL discovery.	2014	mented in [matlab], python a
24407226	r	Enhanced flowType/RchyOptimyx: a BioConductor pipeline for discovery in high-dimensional cytometry data.	2014	ptimyx: a [Bioconductor] pipeline
24371154	c++	MSIsensor: microsatellite instability detection using paired tumor-normal sequence data.	2014	sensor, a [C++] program f
24363381	perl	SurpriseMe: an integrated tool for network community structure characterization using Surprise maximization.	2014	mented in [perl] and c/c++
24363379	java	Ondex Web: web-based visualization and exploration of heterogeneous biological networks.	2014	ritten in [java] and can b
24363378	python	SplicePlot: a utility for visualizing splicing quantitative trait loci.	2014	mented in [python] and is su
24363376	java	JEPETTO: a Cytoscape plugin for gene set enrichment and topological analysis based on interaction networks.	2014	mented in [java] and multi
24363375	c++	GPU-Meta-Storms: computing the structure similarities among massive amount of microbial community samples using GPU.	2014	ture) and [C++]. source c
24359123	c++	A comparison study of succinct data structures for use in GWAS.	2013	veloped a [C++] library,
24351709	python	CrossMap: a versatile tool for coordinate conversion between genome assemblies.	2014	ritten in [python] and c. so
24351708	mathlab	Wigwams: identifying gene modules co-regulated across multiple biological conditions.	2014	a [matlab] implement
24336808	java	ProbeSelect: selecting differentially expressed probes in transcriptional profile data.	2014	mented in [java] and avail
24336807	mathlab	ORCA: a COBRA toolbox extension for model-driven discovery and analysis.	2014	t orca, a [matlab] package,
24336642	r	ChAMP: 450k Chip Analysis Methylation Pipeline.	2014	nted as a [Bioconductor] package i
24336414	c++	BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks.	2014	s in leda [C++], experime
24336146	c++	forqs: forward-in-time simulation of recombination, quantitative traits and selection.	2014	mand-line [C++] program.
24330312	r	Marmal-aid--a database for Infinium HumanMethylation450.	2013	using an [R package] to allow
24308302	python	Processing genome scale tabular data with wormtable.	2013	r data in [python]. wormtabl
24307704	r	Joint estimation of isoform expression and isoform-specific read distribution using multisample RNA-Seq data.	2014	hod in an [R package] called se
24307703	r	Cascade: a R package to study, predict and simulate the diffusion of a signal through a temporal gene network.	2014	ascade: a [R package] to study,
24267918	java	An efficient method for mining cross-timepoint gene regulation sequential patterns from time course gene expression datasets.	2013	sion. the [java] source co
24297519	mathlab	Topological augmentation to infer hidden processes in biological systems.	2014	[matlab] code and
24292941	java	AISAIC: a software suite for accurate identification of significant aberrations in cancers.	2014	escribe a [java] aisaic pa
24292937	r	Exact likelihood computation in Boolean networks with probabilistic time delays, and its application in signal network reconstruction.	2014	atistical [language r]. code and
24281695	c++	Flexible analysis of RNA-seq data using mixed effects models.	2014	ithreaded [C++] programs
24273246	java	Sequence alignment visualization in HTML5 without Java.	2014	5 without [java].
24273246	javascript	Sequence alignment visualization in HTML5 without Java.	2014	html and [javascript] for inter
24273242	c++	jMetalCpp: optimizing molecular docking problems with a C++ metaheuristic framework.	2014	ms with a [C++] metaheuri
24273239	python	Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins.	2014	the [python] analysis
24266924	python	zipHMMlib: a highly optimised HMM library exploiting repetitions in the input to speed up the forward algorithm.	2013	hmm, with [python] bindings
24266924	c++	zipHMMlib: a highly optimised HMM library exploiting repetitions in the input to speed up the forward algorithm.	2013	ithm as a [C++] library,
24257187	mathlab	Effect of separate sampling on classification accuracy.	2014	ritten in [matlab]. a functi
24257186	mathlab	FastPros: screening of reaction knockout strategies for metabolic engineering.	2014	mented in [matlab] and cobra
24256072	r	A novel phenotypic dissimilarity method for image-based high-throughput screens.	2013	ble as an [R package].
24255646	r	Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data.	2014	the [R package] abs filte
24243934	java	ASSIST: a fast versatile local structural comparison tool.	2014	eloped in [java] se 6, wit
24234003	perl	footprintDB: a database of transcription factors with annotated cis elements and binding interfaces.	2014	ed in php,[perl], mysql an
24229408	c++	SUNPLIN: simulation with uncertainty for phylogenetic investigations.	2013	en in the [C++] language.
24227677	r	featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.	2014	ttp://www.[Bioconductor].org) soft
24227674	r	MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments.	2014	antage of [Bioconductor]'s annotat
24222209	r	tRanslatome: an R/Bioconductor package to portray translational control.	2014	ilable in [Bioconductor].
24215025	r	RelateAdmix: a software tool for estimating relatedness between admixed individuals.	2014	nted in c [and R], is freel
24192544	perl	WaveCNV: allele-specific copy number alterations in primary tumors and xenograft models from next-generation sequencing.	2014	plemented [perl].
24192544	mathlab	WaveCNV: allele-specific copy number alterations in primary tumors and xenograft models from next-generation sequencing.	2014	mented in [matlab], and copy
24191071	javascript	Phylowood: interactive web-based animations of biogeographic and phylogeographic histories.	2014	that uses [javascript] to genera
24191069	r	Model-based clustering for RNA-seq data.	2014	an [R package], mbcluste
24177721	python	AnchorMS: a bioinformatics tool to derive structural information from the mass spectra of cross-linked protein complexes.	2014	coded in [python], and is a
24177720	mathlab	MetaboNetworks, an interactive Matlab-based toolbox for creating, customizing and exploring sub-networks from KEGG.	2014	tworks in [matlab] using mai
24177716	python	pyGCluster, a novel hierarchical clustering approach.	2014	requires [python] 2.7, it i
24174567	r	MSPrep--summarization, normalization and diagnostics for processing of mass spectrometry-based metabolomic data.	2014	he msprep [R package] to comple
24167158	r	Direction pathway analysis of large-scale proteomics data reveals novel features of the insulin action pathway.	2014	the [R package] 'directpa
24167156	python	AllergenFP: allergenicity prediction by descriptor fingerprints.	2014	ritten in [python], with giu
24162561	r	Discriminative motif analysis of high-throughput dataset.	2014	e via the [Bioconductor] repositor
24162467	r	Identification of important regressor groups, subgroups and individuals via regularization methods: application to gut microbiome data.	2014	ted in an [R package], which is
24152242	java	Compact representation of k-mer de Bruijn graphs for genome read assembly.	2013	reads. a [java] implement
24149054	java	SeqPig: simple and scalable scripting for large sequencing data sets in Hadoop.	2014	adoop and [java], they are
24149052	java	BEReX: Biomedical Entity-Relationship eXplorer.	2014	tandalone [java] applicati
24149051	r	Exploring high dimensional data with Butterfly: a novel classification algorithm based on discrete dynamical systems.	2014	butterfly [R package]. in the i
24135265	r	A probabilistic approach to explore human miRNA targetome by integrating miRNA-overexpression data and sequence information.	2014	ttp://www.[Bioconductor].org/packa
24135262	mathlab	Automated prior knowledge-based quantification of neuronal patterns in the spinal cord of zebrafish.	2014	en-source [matlab] toolbox g
24132929	r	gCMAP: user-friendly connectivity mapping with R.	2014	ystems at [Bioconductor] (http://w
24130306	java	SecStAnT: secondary structure analysis tool for data selection, statistics and models building.	2014	mented in [java] and suppo
24123675	java	GIIRA--RNA-Seq driven gene finding incorporating ambiguous reads.	2014	mented in [java] and is av
24123674	mathlab	PLIDA: cross-platform gene expression normalization using perturbed topic models.	2014	[matlab] code is a
24123673	r	Two novel pathway analysis methods based on a hierarchical model.	2014	an [R package] is under
24115169	c++	A penalized Bayesian approach to predicting sparse protein-DNA binding landscapes.	2014	mented in [C++] with open
24112435	java	cudaMap: a GPU accelerated program for gene expression connectivity mapping.	2013	a popular [java] applicati
24108186	java	The semantic measures library and toolkit: fast computation of semantic similarity and relatedness using biomedical ontologies.	2014	oviding a [java] library,
24098943	c++	Advances in the REDCAT software package.	2013	oriented [C++] environme
24085566	mathlab	MMAD: microarray microdissection with analysis of differences is a computational tool for deconvoluting cell type-specific contributions from tissue samples.	2014	mented in [matlab] is public
24078713	r	ReportingTools: an automated result processing and presentation toolkit for high-throughput genomic analyses.	2013	gtools, a [Bioconductor] package,
24078702	javascript	STAR: an integrated solution to management and visualization of sequencing data.	2013	leverages [javascript], html5 ca
24078685	java	Lep-MAP: fast and accurate linkage map construction for large SNP datasets.	2013	[java] source co
24072732	java	WebGLORE: a web service for Grid LOgistic REgression.	2013	tes ajax, [java] applet/se
24068035	java	BlastGraph: a comparative genomics tool based on BLAST and graph algorithms.	2013	teractive [java] program f
24064421	r	Methods and challenges in timing chromosomal abnormalities within cancer samples.	2013	ods in an [R package] cancertim
24064420	c++	QSSPN: dynamic simulation of molecular interaction networks describing gene regulation, signalling and whole-cell metabolism in human cells.	2013	mented in [C++] are avail
24064416	python	BioServices: a common Python package to access biological Web Services programmatically.	2013	a common [python] package t
24058058	python	Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold.	2013	n c++ and [python] and can b
24058058	c++	Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold.	2013	ritten in [C++] and pytho
24058055	r	customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search.	2013	prodb: an [R package] to genera
24045775	java	Pattern search in BioPAX models.	2014	eloped in [java]. source c
24015679	r	MultiChIPmixHMM: an R package for ChIP-chip data analysis modeling spatial dependencies and multiple replicates.	2013	ixhmm: an [R package] for chip-
24013927	mathlab	Multi-profile Bayesian alignment model for LC-MS data analysis with integration of internal standards.	2013	[matlab] code, raw
24008417	r	NetWeAvers: an R package for integrative biological network analysis with mass spectrometry data.	2013	avers: an [R package] for integ
24006871	c++	Pathway-PDT: a flexible pathway analysis tool for nuclear families.	2013	mented in [C++] with posi
23995392	c++	PyroHMMvar: a sensitive and accurate method to call short indels and SNPs for Ion Torrent and 454 data.	2013	mented in [C++] and suppo
23995391	c++	Consed: a graphical editor for next-generation sequencing.	2013	ems or as [C++] source co
23990418	r	Multiple alignment-free sequence comparison.	2013	ilable as [R package] named 'mu
23990415	r	A-clustering: a novel method for the detection of co-regulated methylation regions, and regions associated with exposure.	2013	ovide the [R package] aclust th
23986565	r	Identifying differentially expressed proteins in two-dimensional electrophoresis experiments: inputs from transcriptomics statistical tools.	2013	kage from [Bioconductor] (http://w
23981227	r	NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data.	2013	asets and [R package] are avail
23980025	c++	MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples.	2013	mented in [C++] and is av
23975765	python	GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data.	2013	mented in [python] and requi
23975763	java	RNAfbinv: an interactive Java application for fragment-based design of RNA sequences.	2013	teractive [java] applicati
23968174	r	MethyQA: a pipeline for bisulfite-treated methylation sequencing quality assessment.	2013	n in perl [and R]. the pipe
23968174	perl	MethyQA: a pipeline for bisulfite-treated methylation sequencing quality assessment.	2013	ritten in [perl] and r. th
23966112	r	Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge.	2013	ell as an [R package] that impl
23965047	r	A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments.	2013	rt of the [Bioconductor] project a
23962615	c++	fmcsR: mismatch tolerant maximum common substructure searching in R.	2013	mented in [C++]. it inclu
23962615	r	fmcsR: mismatch tolerant maximum common substructure searching in R.	2013	from the [Bioconductor] site (htt
23962281	python	Hierarchical Bayesian modelling of gene expression time series across irregularly sampled replicates and clusters.	2013	mented in [python], and are
23958730	perl	HippDB: a database of readily targeted helical protein-protein interactions.	2013	mented in [perl] and suppo
23958729	r	iBMQ: a R/Bioconductor package for integrated Bayesian modeling of eQTL data.	2013	en-source [R package], ibmq. ou
23958727	r	Efficient inference of local ancestry.	2013	ted as an [R package], which is
23958726	r	RDAVIDWebService: a versatile R interface to DAVID.	2013	ble as an [R package] from the
23958724	r	A new statistic for identifying batch effects in high-throughput genomic data that uses guided principal component analysis.	2013	the gpca [R package] (availabl
23956305	r	A Turing test for artificial expression data.	2013	d via the [CRAN] package a
23956303	c++	SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes.	2013	the boost [C++] libraries
23946504	java	SubNet: a Java application for subnetwork extraction.	2013	subnet: a [java] applicati
23946503	python	omiRas: a Web server for differential expression analysis of miRNAs derived from small RNA-Seq data.	2013	mented in [python], postgres
23946501	python	isomiRID: a framework to identify microRNA isoforms.	2013	mand line [python] script av
23941167	java	ArkMAP: integrating genomic maps across species and data sources.	2013	-updating [java] 'web star
23937229	r	RCircos: an R package for Circos 2D track plots.	2013	ircos: an [R package] for circo
23937229	perl	RCircos: an R package for Circos 2D track plots.	2013	rcos is a [perl] language
23929032	perl	ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq.	2013	mented in [perl] as a comp
23929031	java	PARSEC: PAtteRn SEarch and Contextualization.	2013	mented in [java], javascri
23929031	c++	PARSEC: PAtteRn SEarch and Contextualization.	2013	cript and [C++], with all
23929031	javascript	PARSEC: PAtteRn SEarch and Contextualization.	2013	in java, [javascript] and c++,
23929030	java	WebRASP: a server for computing energy scores to assess the accuracy and stability of RNA 3D structures.	2013	requires [java] plugin fo
23926227	mathlab	OncoSNP-SEQ: a statistical approach for the identification of somatic copy number alterations from next-generation sequencing of cancer genomes.	2013	[matlab] code is a
23926226	r	nCal: an R package for non-linear calibration.	2013	ncal: an [R package] for non-l
23918249	java	The BioPAX Validator.	2013	ine tool, [java] library a
23918247	java	CellMissy: a tool for management, storage and analysis of cell migration data produced in wound healing-like assays.	2013	eloped in [java]. source c
23900188	perl	Indel and Carryforward Correction (ICC): a new analysis approach for processing 454 pyrosequencing data.	2013	mented in [perl] and suppo
23885712	r	DepthTools: an R package for a robust analysis of gene expression data.	2013	tools: an [R package] for a rob
23884480	python	OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes.	2013	nted as a [python] script an
23883280	r	svapls: an R package to correct for hidden factors of variability in gene expression studies.	2013	vapls: an [R package] to correc
23870110	java	Mining differential top-k co-expression patterns from time course comparative gene expression datasets.	2013	sses. the [java] source co
23868956	perl	SAPA tool: finding protein regions by combination of amino acid composition, scaled profiles, patterns and rules.	2013	mented in [perl], html, cs
23868956	javascript	SAPA tool: finding protein regions by combination of amino acid composition, scaled profiles, patterns and rules.	2013	, css and [javascript] and runni
23864731	r	deltaGseg: macrostate estimation via molecular dynamics simulations and multiscale time series analysis.	2013	deltagseg [R package] that perf
23815292	c++	A subgraph isomorphism algorithm and its application to biochemical data.	2013	, and our [C++] implement
23853063	python	Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming.	2013	en-source [python] package t
23846745	java	SICOP: identifying significant co-interaction patterns.	2013	ritten in [java] and accep
23846743	python	pyRMSD: a Python package for efficient pairwise RMSD matrix calculation and handling.	2013	pyrmsd: a [python] package f
23842814	perl	A new framework for computational protein design through cost function network optimization.	2013	(based on [perl] scripts)
23842812	r	A genomic random interval model for statistical analysis of genomic lesion data.	2013	an [R package] will be f
23842806	python	BioSmalltalk: a pure object system and library for bioinformatics.	2013	sage than [biopython] and biope
23842806	perl	BioSmalltalk: a pure object system and library for bioinformatics.	2013	ython and [bioperl] for some
23837715	r	TCC: an R package for comparing tag count data with robust normalization strategies.	2013	tcc: an [R package] for compa
23836142	python	Determining the subcellular location of new proteins from microscope images using local features.	2013	ritten in [python] and c++ a
23836142	c++	Determining the subcellular location of new proteins from microscope images using local features.	2013	ython and [C++] and is av
23832245	java	PhosphoChain: a novel algorithm to predict kinase and phosphatase networks from high-throughput expression data.	2013	mented in [java] and avail
23828785	java	Rapid similarity search of proteins using alignments of domain arrangements.	2014	provide a [java] api for p
23828782	c++	Scalable metagenomic taxonomy classification using a reference genome database.	2013	mented in [C++] and is fr
23825369	r	mRMRe: an R package for parallelized mRMR ensemble feature selection.	2013	mrmre: an [R package] for paral
23825367	r	CellMix: a comprehensive toolbox for gene expression deconvolution.	2013	llmix, an [R package] that inco
23821648	r	Data-based filtering for replicated high-throughput transcriptome sequencing experiments.	2013	ed in the [R package] htsfilter
23818512	python	BNFinder2: Faster Bayesian network learning and Bayesian classification.	2013	mented in [python] and freel
23812989	c++	Predicting protein interactions via parsimonious network history inference.	2013	mented in [C++], is open
23812983	java	Inference of historical migration rates via haplotype sharing.	2013	doris, a [java] implement
23811095	java	LNETWORK: an efficient and effective method for constructing phylogenetic networks.	2013	uilt as a [java] software
23803468	java	Pipit: visualizing functional impacts of structural variations.	2013	-platform [java] applicati
23786769	r	PING 2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data.	2013	en-source [R package], ping 2.0
23786768	python	Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing.	2013	, octave, [python] and c) fo
23786768	mathlab	Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing.	2013	ckage (in [matlab], octave,
23786315	python	Bioinformatic pipelines in Python with Leaf.	2013	elines in [python] with leaf
23782613	java	GPViz: dynamic visualization of genomic regions and variants affecting protein domains.	2013	based on [java] 7 and can
23772051	r	AdvISER-PYRO: Amplicon Identification using SparsE Representation of PYROsequencing signal.	2013	ted in an [R package] (http://s
23766418	java	Metingear: a development environment for annotating genome-scale metabolic models.	2013	mented in [java] with bund
23766417	java	UniNovo: a universal tool for de novo peptide sequencing.	2013	mented in [java] and teste
23763826	java	KNODWAT: a scientific framework application for testing knowledge discovery methods for the biomedical domain.	2013	ed, using [java] on spring
23758891	r	Utilizing protein structure to identify non-random somatic mutations.	2013	logy. the [R package] is availa
23758828	c	QualComp: a new lossy compressor for quality scores based on rate distortion theory.	2013	package, [written in C] and freel
23758781	javascript	bioWeb3D: an online webGL 3D data visualisation tool.	2013	ritten in [javascript], bioweb3d
23735186	python	A mixture model for expression deconvolution from RNA-seq in heterogeneous tissues.	2013	ritten in [python], and is f
23735122	python	Software tool for 3D extraction of germinal centers.	2013	ritten in [python] with c ex
23749961	java	NOA: a cytoscape plugin for network ontology analysis.	2013	n source, [java] program f
23749960	javascript	Network2Canvas: network visualization on a canvas with enrichment analysis.	2013	with the [javascript] library d
23749958	r	PurBayes: estimating tumor cellularity and subclonality in next-generation sequencing data.	2013	ted as an [R package], and sour
23742985	perl	Automated design of paralogue ratio test assays for the accurate and rapid typing of copy number variation.	2013	forms: a [perl] script (v
23742983	python	REDItools: high-throughput RNA editing detection made easy.	2013	suite of [python] scripts t
23740750	r	Pathview: an R/Bioconductor package for pathway-based data integration and visualization.	2013	e through [Bioconductor] and r-for
23740744	r	opm: an R package for analysing OmniLog(R) phenotype microarray data.	2013	opm: an [R package] for analy
23740742	java	WhichCyp: prediction of cytochromes P450 inhibition.	2013	whichcyp [java] program a
23736531	c++	NGS++: a library for rapid prototyping of epigenomics software tools.	2013	ritten in [C++] using the
23732275	javascript	Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool.	2013	ritten in [javascript] on the cl
23732273	c++	SPANNER: taxonomic assignment of sequences using pyramid matching of similarity profiles.	2013	[C++] source co
23720490	r	Drug-target interaction prediction through domain-tuned network-based inference.	2013	hrough an [R package] at the fo
23712657	c	DeMix: deconvolution for mixed cancer transcriptomes using raw measured data.	2013	codes are [written in C] and integ
23709497	r	viRome: an R package for the visualization and analysis of viral small RNA sequence datasets.	2013	irome: an [R package] for the v
23709494	r	Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences.	2013	[R package] 'triplex'
23681123	r	TANGO: a generic tool for high-throughput 3D image analysis for studying nuclear organization.	2013	analysis [and R] (http://c
23677940	python	Identification of hidden relationships from the coupling of hydrophobic cluster analysis and domain architecture information.	2013	mented in [python] v2.7 and
23658420	java	Twine: display and analysis of cis-regulatory modules.	2013	wine is a [java] gui with
23652425	python	pyGenClean: efficient tool for genetic data clean up before association testing.	2013	en source [python] 2.7 softw
23645815	java	RegaDB: community-driven data management and analysis for infectious diseases.	2013	en in the [java] programmi
23640718	mathlab	miMsg: a target enrichment algorithm for predicted miR-mRNA interactions based on relative ranking of matched expression data.	2013	[matlab] source co
23630177	mathlab	Intervention in gene regulatory networks with maximal phenotype alteration.	2013	results, [matlab] source co
23627667	r	Steiner tree methods for optimal sub-network identification: an empirical study.	2013	nernet on [CRAN] (http://w
23625999	c++	NetworkTrail--a web service for identifying and visualizing deregulated subnetworks.	2013	mented in [C++]. networkt
23620362	r	RSVSim: an R/Bioconductor package for the simulation of structural variations.	2013	ttp://www.[Bioconductor].org. a vi
23617841	r	Empirical Bayesian analysis of paired high-throughput sequencing data with a beta-binomial distribution.	2013	able from [Bioconductor] (http://w
23617301	java	D-Light on promoters: a client-server system for the analysis and visualization of cis-regulatory elements.	2013	mented in [java] and provi
23617269	mathlab	Ensemble-based prediction of RNA secondary structures.	2013	our data, [matlab] software
23617239	c++	An efficient algorithm to perform multiple testing in epistasis screening.	2013	mented in [C++] in our ep
23613487	python	mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters.	2013	age/ as a [python] package a
23595665	r	CellH5: a format for data exchange in high-content screening.	2013	nd at www.[Bioconductor].org/packa
23595662	javascript	A self-updating road map of The Cancer Genome Atlas.	2013	gine uses [javascript] in conjun
23595660	r	Learning gene network structure from time laps cell imaging in RNAi Knock downs.	2013	rt of the [Bioconductor] r-package
23589650	r	Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size.	2013	.html and [Bioconductor].
23589649	mathlab	Exome-based analysis for RNA epigenome sequencing data.	2013	the [matlab] package '
23586463	javascript	Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool.	2013	using the [javascript] library,
23577585	r	Random forest methodology for model-based recursive partitioning: the mobForest package for R.	2013	resent an [R package] called m
23575005	r	An efficient post-hoc integration method improving peak alignment of metabolomics data from GCxGC/TOF-MS.	2013	measures. [R package] and examp
23574737	javascript	Biographer: web-based editing and rendering of SBGN compliant biochemical networks.	2013	, css and [javascript] and can b
23574736	mathlab	OKVAR-Boost: a novel boosting algorithm to infer nonlinear dynamics and interactions in gene regulatory networks.	2013	var-boost [matlab] code is a
23564846	java	MonaLisa--visualization and analysis of functional modules in biochemical networks.	2013	at least [java] 6 and run
23564843	python	LibSBMLSim: a reference implementation of fully functional SBML simulator.	2013	java, c#, [python] and ruby)
23564843	c	LibSBMLSim: a reference implementation of fully functional SBML simulator.	2013	ed in the [C programming] language
23560875	r	An AUC-based permutation variable importance measure for random forests.	2013	ed in the [R package] party for
23559638	python	Bayesian hierarchical model of protein-binding microarray k-mer data reduces noise and identifies transcription factor subclasses and preferred k-mers.	2013	and r and [python] scripts a
23559638	r	Bayesian hierarchical model of protein-binding microarray k-mer data reduces noise and identifies transcription factor subclasses and preferred k-mers.	2013	iled code [and R] and pytho
23557111	c++	CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions.	2013	n in cuda [C++] and ptx a
23543414	r	Fast simulation of reconstructed phylogenies under global time-dependent birth-death processes.	2013	ed in the [R package] tess, ava
23539306	java	FishingCNV: a graphical software package for detecting rare copy number variations in exome-sequencing data.	2013	ted using [java] 1.6. it c
23508970	mathlab	The Simmune Modeler visual interface for creating signaling networks based on bi-molecular interactions.	2013	port into [matlab].
23508967	mathlab	SRV: an open-source toolbox to accelerate the recovery of metabolic biomarkers and correlations from metabolic phenotyping datasets.	2013	en-source [matlab] and gnu o
23505297	c++	TfReg: calculating DNA and RNA melting temperatures and opening profiles with mesoscopic models.	2013	xtensible [C++] implement
23505296	python	Programming strategy for efficient modeling of dynamics in a population of heterogeneous cells.	2013	complete [python] code is a
23505295	c++	HAL: a hierarchical format for storing and analyzing multiple genome alignments.	2013	rehensive [C++] api. a se
23505294	mathlab	Identification of cancer fusion drivers using network fusion centrality.	2013	[matlab] code impl
23505292	java	Brain: biomedical knowledge manipulation.	2013	rain is a [java] software
23493324	python	ChemoPy: freely available python package for computational biology and chemoinformatics.	2013	available [python] package f
23493321	perl	Modeling risk stratification in human cancer.	2013	tation in [perl], r and ap
23479353	java	JAWAMix5: an out-of-core HDF5-based java implementation of whole-genome association studies using mixed models.	2013	df5-based [java] implement
23476023	c	Specificity and affinity quantification of protein-protein interactions.	2013	mented in [C language], and the
23471300	python	freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers.	2013	equires a [python] interpret
23471300	c++	freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers.	2013	ter and a [C++] compiler.
23452827	perl	BioTile, a Perl based tool for the identification of differentially enriched regions in tiling microarray data.	2013	iotile, a [perl] based too
23452776	r	virtualArray: a R/bioconductor package to merge raw data from different microarray platforms.	2013	bi geo or [Bioconductor]. after es
23452721	c++	MethylPCA: a toolkit to control for confounders in methylome-wide association studies.	2013	sks, uses [C++] for cpu a
23449093	r	SplicingCompass: differential splicing detection using RNA-seq data.	2013	atistical [language r] at http:/
23435069	javascript	BioJS: an open source JavaScript framework for biological data visualization.	2013	en source [javascript] framework
23434837	mathlab	An improved constraint filtering technique for inferring hidden states and parameters of a biological model.	2013	[matlab] code avai
23428642	r	DeconRNASeq: a statistical framework for deconvolution of heterogeneous tissue samples based on mRNA-Seq data.	2013	naseq, an [R package] for decon
23428641	r	EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments.	2013	an [R package] containin
23426256	python	propy: a tool to generate various modes of Chou's PseAAC.	2013	en source [python] package c
23422340	mathlab	IRootLab: a free and open-source MATLAB toolbox for vibrational biospectroscopy data analysis.	2013	en-source [matlab] toolbox f
23419378	java	PleioGRiP: genetic risk prediction with pleiotropy.	2013	mented in [java], and it i
23419376	r	Nozzle: a report generation toolkit for data analysis pipelines.	2013	ozzle, an [R package] that prov
23419375	r	PLRS: a flexible tool for the joint analysis of DNA copy number and mRNA expression data.	2013	ted as an [R package] and avail
23419374	java	Non-parametric Bayesian approach to post-translational modification refinement of predictions from tandem mass spectrometry.	2013	mented in [java] and is fr
23418188	mathlab	Chemical rule-based filtering of MS/MS spectra.	2013	the [matlab] source co
23418185	python	eMZed: an open source framework in Python for rapid and interactive development of LC/MS data analysis workflows.	2013	mework in [python] for rapid
23413438	r	Efficient comparison of sets of intervals with NC-lists.	2013	, where q [and R] are the s
23368970	java	An extensible six-step methodology to automatically generate fuzzy DSSs for diagnostic applications.	2013	alized in [java] following
23396124	mathlab	Quantifying spatial relationships from whole retinal images.	2013	the [matlab] code for
23396123	javascript	MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships.	2013	html and [javascript] with all
23396118	r	displayHTS: a R package for displaying data and results from high-throughput screening experiments.	2013	layhts: a [R package] for displ
23394478	c	Multiple consensus trees: a method to separate divergent genes.	2013	us trees, [written in C] was made
23391497	python	Coalescent simulation in continuous space.	2013	available [python] module.
23390138	c++	Fast thermodynamically constrained flux variability analysis.	2013	ritten in [C++] and publi
23390138	mathlab	Fast thermodynamically constrained flux variability analysis.	2013	exists a [matlab] interface
23379655	r	puma 3.0: improved uncertainty propagation methods for gene and transcript expression analysis.	2013	tion. the [Bioconductor] package p
23375020	python	FANTOM: Functional and taxonomic analysis of metagenomes.	2013	mented in [python], is platf
23365410	python	MosaicFinder: identification of fused gene families in sequence similarity networks.	2013	ed in the [python] program f
23365410	c++	MosaicFinder: identification of fused gene families in sequence similarity networks.	2013	od in the [C++] program m
23355290	c++	Bellman's GAP--a language and compiler for dynamic programming in sequence analysis.	2013	iled into [C++] code that
23331614	python	Genecentric: a package to uncover graph-theoretic structure in high-throughput epistasis data.	2013	ted bpms. [python] is the on
23329415	java	SBSI: an extensible distributed software infrastructure for parameter estimation in systems biology.	2013	ritten in [java] and are p
23327649	javascript	Kerfuffle: a web tool for multi-species gene colocalization analysis.	2013	mented in [javascript] (using jq
23324080	java	JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison.	2013	file and [java] webstart.
23323831	r	GSVA: gene set variation analysis for microarray and RNA-seq data.	2013	rt of the [Bioconductor] project a
23323543	r	SRAdb: query and use public next-generation sequencing data from within R.	2013	sradb [Bioconductor] package p
23320794	r	Sources of variation in false discovery rate estimation include sample size, correlation, and inherent differences between groups.	2012	(umpire) [R package]. we estim
23314326	c++	Reconciling differential gene expression data with molecular interaction networks.	2013	[C++] software
23314324	python	NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets.	2013	systems. [python] 2.6+ and
23314322	perl	gKaKs: the pipeline for genome-level Ka/Ks calculation.	2013	mented in [perl] and is fr
23314125	r	CePa: an R package for finding significant pathways weighted by multiple network centralities.	2013	cepa: an [R package] for findi
23303511	java	Fragment recruitment on metabolic pathways: comparative metabolic profiling of metagenomes and metatranscriptomes.	2013	-friendly [java] program f
23303510	r	HitWalker: variant prioritization for personalized functional cancer genomics.	2013	ble as an [R package] from www.
23303509	python	ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies.	2013	in c and [python].
23303508	python	Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine.	2013	mented in [python] (v2.6) an
23303507	r	SIBER: systematic identification of bimodally expressed genes using RNAseq data.	2013	the [R package] siber is
23282007	mathlab	CFMDS: CUDA-based fast multidimensional scaling for genome-scale data.	2012	ng c# and [matlab]. in our e
23300135	perl	MaSC: mappability-sensitive cross-correlation for estimating mean fragment length of single-end short-read sequencing data.	2013	en-source [perl] implement
23292739	mathlab	KEGGParser: parsing and editing KEGG pathway maps in Matlab.	2013	y maps in [matlab].
23274212	r	rBiopaxParser--an R package to parse, modify and visualize BioPAX data.	2013	arser--an [R package] to parse,
25937946	mathlab	Exploiting identifiability and intergene correlation for improved detection of differential expression.	2013	rithms in [matlab] and in r
23271269	mathlab	Inference of gene regulatory networks from genome-wide knockout fitness data.	2013	[matlab] code and
23267175	c++	Ultranet: efficient solver for the sparse inverse covariance selection problem in gene network modeling.	2013	mented in [C++] and avail
23267174	r	Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments.	2013	cellassay [R package] available
23242262	java	Minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers.	2013	original [java] implement
23242262	python	Minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers.	2013	nd its r, [python] and matla
23242262	c++	Minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers.	2013	ctave and [C++]. the c so
23242262	r	Minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers.	2013	g for the [R package] minerva.
23242262	mathlab	Minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers.	2013	ython and [matlab] wrappers.
23233655	perl	Characterization of disordered proteins with ENSEMBLE.	2013	dded in a [perl] wrapper.
23220574	python	Nestly--a framework for running software with nested parameter choices and aggregating results.	2013	nestly, a [python] package t
23216942	r	A novel approach for biomarker selection and the integration of repeated measures experiments from two assays.	2012	ed in the [R package] mixomics
23216884	perl	Flexible and efficient genome tiling design with penalized uniqueness score.	2012	nted as a [perl] program,
23202745	r	BlueSNP: R package for highly scalable genome-wide association studies using Hadoop clusters.	2013	bluesnp: [R package] for highl
23178637	java	Bioclipse-R: integrating management and visualization of life science data with statistical analysis.	2013	a set of [java] plug-ins
23178637	r	Bioclipse-R: integrating management and visualization of life science data with statistical analysis.	2013	ogramming [language r]. the syne
23176119	r	A tutorial in displaying mass spectrometry-based proteomic data using heat maps.	2012	ogramming [language r], which ca
23175757	mathlab	An effective framework for reconstructing gene regulatory networks from genetical genomics data.	2013	a [matlab] implement
23172864	javascript	Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web.	2013	mented in [javascript] with all
23172861	java	DOOSS: a tool for visual analysis of data overlaid on secondary structures.	2013	ritten in [java] and is av
23164367	c++	Estimating relative abundances of proteins from shotgun proteomics data.	2012	eins. the [C++] source co
23162084	java	An application of a relational database system for high-throughput prediction of elemental compositions from accurate mass values.	2013	mented in [java], mysql, a
23162059	java	VAGUE: a graphical user interface for the Velvet assembler.	2013	rgets the [java] virtual m
23162058	perl	VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue.	2013	mented in [perl] and is av
23162057	c++	Largenet2: an object-oriented programming library for simulating large adaptive networks.	2013	largenet2 [C++] library p
23151154	r	Clustering of time-course gene expression profiles using normal mixture models with autoregressive random effects.	2012	developed [R package] is flexib
23148484	c++	Oculus: faster sequence alignment by streaming read compression.	2012	dependent [C++] source co
23137144	r	Isotope pattern deconvolution for peptide mass spectrometry by non-negative least squares/least absolute deviation template matching.	2012	orms. the [R package] ippd impl
23129301	java	HD-CNV: hotspot detector for copy number variants.	2013	en source [java] code and
23129297	r	DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data.	2013	[R package] (submitte
23113980	r	A novel algorithm for simultaneous SNP selection in high-dimensional genome-wide association studies.	2012	nking. an [R package] implement
23110970	java	13CFLUX2--high-performance software suite for (13)C-metabolic flux analysis.	2013	ard) with [java] and pytho
23110970	python	13CFLUX2--high-performance software suite for (13)C-metabolic flux analysis.	2013	java and [python] add-ons t
23110970	c++	13CFLUX2--high-performance software suite for (13)C-metabolic flux analysis.	2013	mented in [C++] (iso/iec
23109181	java	ADAM: automated data management for research datasets.	2013	ted using [java] and suppo
23104889	mathlab	SPSens: a software package for stochastic parameter sensitivity analysis of biochemical reaction networks.	2013	face with [matlab], and seve
23104886	c++	STAR: ultrafast universal RNA-seq aligner.	2013	tandalone [C++] code. sta
23104885	java	XiP: a computational environment to create, extend and share workflows.	2013	oth r and [java], the anal
23102059	java	Combing the hairball with BioFabric: a new approach for visualization of large networks.	2012	en-source [java] applicati
23097421	python	FFPopSim: an efficient forward simulation package for the evolution of large populations.	2012	ses and a [python] interface
23097421	c++	FFPopSim: an efficient forward simulation package for the evolution of large populations.	2012	ection of [C++] classes a
23097420	r	AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data.	2013	lable via [Bioconductor] at the ur
23093610	c++	Genotype calling and phasing using next-generation sequencing reads and a haplotype scaffold.	2013	nted in a [C++] program a
23083219	r	dsPIG: a tool to predict imprinted genes from the deep sequencing of whole transcriptomes.	2012	ovided an [R package] for dspig
23046475	perl	Transcriptome profile of a bovine respiratory disease pathogen: Mannheimia haemolytica PHL213.	2012	nd custom [perl] scripts i
23046276	java	BirdsEyeView (BEV): graphical overviews of experimental data.	2012	able as a [java] webstart
23052038	perl	Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches.	2012	ted using [perl] scripts a
23047557	c++	SCALCE: boosting sequence compression algorithms using locally consistent encoding.	2012	mented in [C++] with both
23044551	c++	COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly.	2012	mented in [C++] and is fr
23044545	r	fRMA ST: frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays.	2012	rough the [Bioconductor] project.
23044544	c++	KGBassembler: a karyotype-based genome assembler for Brassicaceae species.	2012	mented in [C++] with a gr
23044538	c++	MesoRD 1.0: Stochastic reaction-diffusion simulations in the microscopic limit.	2012	ritten in [C++] and licen
23043260	python	Frnakenstein: multiple target inverse RNA folding.	2012	nted as a [python] program c
23031277	java	VarioML framework for comprehensive variation data representation and exchange.	2012	d data. a [java] implement
23023981	perl	FeatureStack: Perl module for comparative visualization of gene features.	2012	urestack: [perl] module fo
23020243	r	QUAliFiER: an automated pipeline for quality assessment of gated flow cytometry data.	2012	ssible to [Bioconductor]'s computa
23014632	c	SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences.	2012	olpred is [written in C] and is av
23014630	r	integIRTy: a method to identify genes altered in cancer by accounting for multiple mechanisms of regulation using item response theory.	2012	the [R package] integirty
22989518	java	MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays.	2012	en-source [java] library j
22982574	mathlab	Efficient methods for identifying mutated driver pathways in cancer.	2012	a [matlab] package o
22982573	java	DLRS: gene tree evolution in light of a species tree.	2012	lable for [java] se 6+ und
22982573	c++	DLRS: gene tree evolution in light of a species tree.	2012	tly older [C++] version a
22976081	c++	Phylogenetics, likelihood, evolution and complexity.	2012	mented in [C++] and suppo
22976081	perl	Phylogenetics, likelihood, evolution and complexity.	2012	accessory [perl] scripts a
22974078	r	Analysis of tiling array expression studies with flexible designs in Bioconductor (waveTiling).	2012	esigns in [Bioconductor] (wavetili
22962481	c++	Imaging, quantification and visualization of spatio-temporal patterning in mESC colonies under different culture conditions.	2012	plemented [C++] and mathe
22962477	mathlab	Comprehensive estimation of input signals and dynamics in biochemical reaction networks.	2012	[matlab] code is a
22962475	python	Random sampling of elementary flux modes in large-scale metabolic networks.	2012	tation in [python] is freely
22962461	mathlab	Multiple instance learning of Calmodulin binding sites.	2012	[matlab] code for
22962456	c++	Evolution of gene neighborhoods within reconciled phylogenies.	2012	[C++] implement
22962455	mathlab	Nonlinear dimension reduction with Wright-Fisher kernel for genotype aggregation and association mapping.	2012	mented in [matlab]. source c
22962454	java	An exome sequencing pipeline for identifying and genotyping common CNVs associated with disease with application to psoriasis.	2012	mented in [java] and r and
22962454	r	An exome sequencing pipeline for identifying and genotyping common CNVs associated with disease with application to psoriasis.	2012	d in java [and R] and is fr
22962447	c++	Long read alignment based on maximal exact match seeds.	2012	ritten in [C++], and all
22962345	python	Pythoscape: a framework for generation of large protein similarity networks.	2012	mented in [python] for proce
22962343	java	ImgLib2--generic image processing in Java.	2012	essing in [java].
22954632	python	Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values.	2012	ool and a [python] library t
22946927	r	ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data.	2012	package, [written in R] and avail
22945789	java	JEnsembl: a version-aware Java API to Ensembl data systems.	2012	ion-aware [java] api to en
22945789	perl	JEnsembl: a version-aware Java API to Ensembl data systems.	2012	-specific [perl] apis for
22942023	python	CSB: a Python framework for structural bioinformatics.	2012	csb: a [python] framework
22942019	r	A robust model for read count data in exome sequencing experiments and implications for copy number variant calling.	2012	d into an [R package] called ex
22923307	r	FacPad: Bayesian sparse factor modeling for the inference of pathways responsive to drug treatment.	2012	the [R package] 'facpad'
22923303	r	COMPADRE: an R and web resource for pathway activity analysis by component decompositions.	2012	adre. the [R package] is also a
22923296	c	HiTC: exploration of high-throughput 'C' experiments.	2012	hroughput ['C'] experimen
22923296	r	HiTC: exploration of high-throughput 'C' experiments.	2012	the [R package] hitc is a
22923295	c++	RazerS 3: faster, fully sensitive read mapping.	2012	mented in [C++] and openm
22923294	java	The GlycomeAtlas tool for visualizing and querying glycome data.	2012	site as a [java] applet, i
22923293	python	TRFolder-W: a web server for telomerase RNA structure prediction in yeast genomes.	2012	mand-line [python] toolkit f
22914219	mathlab	Intensity quantile estimation and mapping--a novel algorithm for the correction of image non-uniformity bias in HCS data.	2012	[matlab] function
22914218	java	Qualimap: evaluating next-generation sequencing alignment data.	2012	alimap, a [java] applicati
22909249	python	Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython.	2012	e built a [python] software
22892030	java	SDAR: a practical tool for graphical analysis of two-dimensional data.	2012	ftware in [java] with a us
22877864	java	PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data.	2012	dependent [java] applicati
22877863	java	BioJava: an open-source framework for bioinformatics in 2012.	2012	ta in the [java] programmi
22870940	r	Comparison of methods to detect copy number alterations in cancer using simulated and real genotyping data.	2012	it in an [R package] called cn
22863767	mathlab	Identifying multi-layer gene regulatory modules from multi-dimensional genomic data.	2012	mented by [matlab] is freely
22863766	r	An R package suite for microarray meta-analysis in quality control, differentially expressed gene analysis and pathway enrichment detection.	2012	an [R package] suite for
22856649	java	A resource for benchmarking the usefulness of protein structure models.	2012	irements: [java] runtime e
22856649	perl	A resource for benchmarking the usefulness of protein structure models.	2012	); mysql, [perl] dbi and d
22856649	javascript	A resource for benchmarking the usefulness of protein structure models.	2012	se); php, [javascript], jmol scr
22847934	mathlab	A MATLAB toolbox for structural kinetic modeling.	2012	a [matlab] toolbox f
22847932	r	easyRNASeq: a bioconductor package for processing RNA-Seq data.	2012	aseq', an [R package] that simp
22846331	r	Estimation of sequencing error rates in short reads.	2012	ted in an [R package], which ca
22820205	python	ANGES: reconstructing ANcestral GEnomeS maps.	2012	suite of [python] programs
22820202	java	SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts.	2012	tion is a [java] program t
22815360	r	DanteR: an extensible R-based tool for quantitative analysis of -omics data.	2012	graphical [R package] that feat
22815359	python	Quantifying uniformity of mapped reads.	2012	en source [python] script th
22800377	c++	Slim-filter: an interactive Windows-based application for illumina genome analyzer data assessment and manipulation.	2012	ritten in [C++] and is co
22796960	r	GAPIT: genome association and prediction integrated tool.	2012	eloped an [R package] called ge
22796958	r	A regression model for estimating DNA copy number applied to capture sequencing data.	2012	nted in c [and R] and the c
22796955	r	MALDIquant: a versatile R package for the analysis of mass spectrometry data.	2012	versatile [R package] for the a
22789589	r	iBBiG: iterative binary bi-clustering of gene sets.	2012	ed in the [Bioconductor] package i
22788675	java	A graph-based approach for designing extensible pipelines.	2012	n and the [java] executabl
22782551	r	Efficient sampling for Bayesian inference of conjunctive Bayesian networks.	2012	an [R package] including
22782546	java	CytoSPADE: high-performance analysis and visualization of high-dimensional cytometry data.	2012	, c++ and [java].
22782546	c++	CytoSPADE: high-performance analysis and visualization of high-dimensional cytometry data.	2012	ted in r, [C++] and java.
22782546	r	CytoSPADE: high-performance analysis and visualization of high-dimensional cytometry data.	2012	g and via [Bioconductor] version 2
22772947	mathlab	TLM-Tracker: software for cell segmentation, tracking and lineage analysis in time-lapse microscopy movies.	2012	ilable as [matlab] code or e
22743227	perl	PurityEst: estimating purity of human tumor samples using next-generation sequencing data.	2012	mented in [perl] and is av
22743226	python	RSeQC: quality control of RNA-seq experiments.	2012	ritten in [python] and c. so
22743223	mathlab	A bioimage informatics approach to automatically extract complex fungal networks.	2012	the [matlab] toolbox i
22734019	r	Integrating literature-constrained and data-driven inference of signalling networks.	2012	ed in the [R package] cnorfeede
22730434	python	gSearch: a fast and flexible general search tool for whole-genome sequencing.	2012	ruby and [python].
22730434	perl	gSearch: a fast and flexible general search tool for whole-genome sequencing.	2012	s such as [perl], ruby and
22716030	c++	EGNAS: an exhaustive DNA sequence design algorithm.	2012	ized in a [C++] program.
22713124	r	Down-weighting overlapping genes improves gene set analysis.	2012	ted as an [R package] available
22702410	r	Bios2mds: an R package for comparing orthologous protein families by metric multidimensional scaling.	2012	s2mds: an [R package] for compa
22698142	python	Simulating gene-gene and gene-environment interactions in complex diseases: Gene-Environment iNteraction Simulator 2.	2012	ritten in [python] language
22694346	r	Bayesian model to detect phenotype-specific genes for copy number data.	2012	eloped an [R package], called b
22692220	r	mcaGUI: microbial community analysis R-Graphical User Interface (GUI).	2012	ttp://www.[Bioconductor].org/packa
22689766	mathlab	Nonparametric Bayesian inference for perturbed and orthologous gene regulatory networks.	2012	mented in [matlab] and are a
22689388	r	synbreed: a framework for the analysis of genomic prediction data using R.	2012	t a novel [R package] named syn
22682516	r	ROCS: a reproducibility index and confidence score for interaction proteomics studies.	2012	ble as an [R package] called r
22676372	c++	PollenCALC: software for estimation of pollen compatibility of self-incompatible allo- and autotetraploid species.	2012	ritten in [C++] programmi
22668791	mathlab	Borrowing strength: a likelihood ratio test for related sparse signals.	2012	the [matlab] code is a
22668789	r	SYNCSA--R tool for analysis of metacommunities based on functional traits and phylogeny of the community components.	2012	csa is an [R package] for the a
22668788	python	DiNuP: a systematic approach to identify regions of differential nucleosome positioning.	2012	mented in [python] and is fr
22661647	java	BioMercator V3: an upgrade of genetic map compilation and quantitative trait loci meta-analysis algorithms.	2012	mented in [java] and freel
22647087	python	PyMS: a Python toolkit for processing of gas chromatography-mass spectrometry (GC-MS) data. Application and comparative study of selected tools.	2012	pyms: a [python] toolkit f
22647057	r	Detection and correction of probe-level artefacts on microarrays.	2012	step. an [R package] is freely
22645166	python	An integrated open framework for thermodynamics of reactions that combines accuracy and coverage.	2012	mented in [python], mysql, a
22635606	java	Gowinda: unbiased analysis of gene set enrichment for genome-wide association studies.	2012	mented in [java] (v1.6) an
22635605	r	BATMAN--an R package for the automated quantification of metabolites from nuclear magnetic resonance spectra using a Bayesian model.	2012	atman--an [R package] for the a
22624611	java	TreeSnatcher plus: capturing phylogenetic trees from images.	2012	ui-driven [java] applicati
22607271	java	Natural product-likeness score revisited: an open-source, open-data implementation.	2012	tandalone [java] package f
22607234	c++	Multiple structure alignment with msTALI.	2012	ions. the [C++] source co
22595209	r	flowPeaks: a fast unsupervised clustering for flow cytometry data via K-means and density peak finding.	2012	the [R package] flowpeaks
22595208	mathlab	Robust identification of transcriptional regulatory networks using a Gibbs sampler on outlier sum statistic.	2012	s sampler [matlab] package i
22595207	r	R/EBcoexpress: an empirical Bayesian framework for discovering differential co-expression.	2012	ndziorski [using R], a freely
22594948	r	rCUR: an R package for CUR matrix decomposition.	2012	rcur: an [R package] for cur m
22594911	java	Workflows for microarray data processing in the Kepler environment.	2012	thon, and [java] programmi
22594911	python	Workflows for microarray data processing in the Kepler environment.	2012	in the r, [python], and java
22592383	r	Fast computation for genome-wide association studies using boosted one-step statistics.	2012	the [R package] 'boss' is
22591016	c++	Handling the data management needs of high-throughput sequencing data: SpeedGene, a compression algorithm for the efficient storage of genetic data.	2012	provide a [C++] implement
22581181	r	SRMA: an R package for resequencing array data analysis.	2012	srma: an [R package] for reseq
22581178	r	iFad: an integrative factor analysis model for drug-pathway association inference.	2012	the [R package] 'ifad' an
22581176	c++	Software support for SBGN maps: SBGN-ML and LibSBGN.	2012	ilable in [C++] and java)
22576175	r	CalMaTe: a method and software to improve allele-specific copy number of SNP arrays for downstream segmentation.	2012	en-source [R package] calmate,
22568821	java	PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods.	2012	dependent [java] software
22563068	r	Joint Bayesian inference of condition-specific miRNA and transcription factor activities from combined gene and microRNA expression data.	2012	ed in the [R package] birta, wh
22563066	python	Identifying differentially expressed transcripts from RNA-seq data with biological variation.	2012	n c++ and [python]. the soft
22563066	c++	Identifying differentially expressed transcripts from RNA-seq data with biological variation.	2012	ritten in [C++] and pytho
22559915	c++	EpiFire: An open source C++ library and application for contact network epidemiology.	2012	en source [C++] library a
22559006	r	Matching of array CGH and gene expression microarray features for the purpose of integrative genomic analyses.	2012	able from [Bioconductor].
22536965	python	CONS-COCOMAPS: a novel tool to measure and visualize the conservation of inter-residue contacts in multiple docking solutions.	2012	ritten in [python], taking a
22543499	mathlab	Truncated branch and bound achieves efficient constraint-based genetic design.	2012	ted using [matlab] and is fr
22543367	java	Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.	2012	mented in [java] and suppo
22543366	java	DAVID-WS: a stateful web service to facilitate gene/protein list analysis.	2012	ritten in [java], perl, py
22543366	python	DAVID-WS: a stateful web service to facilitate gene/protein list analysis.	2012	va, perl, [python] and matla
22543366	perl	DAVID-WS: a stateful web service to facilitate gene/protein list analysis.	2012	in java, [perl], python a
22539671	python	DecoyFinder: an easy-to-use python GUI application for building target-specific decoy sets.	2012	sy-to-use [python] gui appli
22539669	python	Statistical interpretation of machine learning-based feature importance scores for biomarker discovery.	2012	[python] source co
22539669	mathlab	Statistical interpretation of machine learning-based feature importance scores for biomarker discovery.	2012	ll as the [matlab] scripts u
22539667	java	CNVRuler: a copy number variation-based case-control association analysis tool.	2012	ams r and [java] from sun
22539666	perl	PSI-Search: iterative HOE-reduced profile SSEARCH searching.	2012	ritten in [perl] for linux
22531217	c++	Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm.	2012	ritten in [C++], licensed
22531214	perl	NuST: analysis of the interplay between nucleoid organization and gene expression.	2012	template [perl] code for
22513995	r	NanoStringNorm: an extensible R package for the pre-processing of NanoString mRNA and miRNA data.	2012	xtensible [R package] for the p
22513994	r	TSSi--an R package for transcription start site identification from 5' mRNA tag data.	2012	tssi--an [R package] for trans
22513993	c++	INRICH: interval-based enrichment analysis for genome-wide association studies.	2012	tandalone [C++] program,
22508794	c++	pIRS: Profile-based Illumina pair-end reads simulator.	2012	ritten in [C++] and perl,
22508794	perl	pIRS: Profile-based Illumina pair-end reads simulator.	2012	n c++ and [perl], and is f
22507266	r	'maskBAD'--a package to detect and remove Affymetrix probes with binding affinity differences.	2012	friendly [R package], compatib
22500002	java	Bpipe: a tool for running and managing bioinformatics pipelines.	2012	ring only [java] as a depe
22500001	c++	optiCall: a robust genotype-calling algorithm for rare, low-frequency and common variants.	2012	mented in [C++] for use o
22492646	mathlab	CRNreals: a toolbox for distinguishability and identifiability analysis of biochemical reaction networks.	2012	e popular [matlab] computati
22492641	r	Differential variability improves the identification of cancer risk markers in DNA methylation studies profiling precursor cancer lesions.	2012	able from [CRAN] (www.r-pr
22492640	java	PaGeFinder: quantitative identification of spatiotemporal pattern genes.	2012	nloadable [java] programs
22492638	r	Detection of differentially expressed segments in tiling array data.	2012	the [R package] including
22492314	java	Eoulsan: a cloud computing-based framework facilitating high throughput sequencing analyses.	2012	mented in [java], supporte
22492311	r	Rknots: topological analysis of knotted biopolymers with R.	2012	flexible [R package] providing
22479706	c++	Network-based functional enrichment.	2011	mented in [C++] and are f
22467912	r	Reno: regularized non-parametric analysis of protein lysate array data.	2012	ogramming [language r] is availa
22467906	c++	OCAP: an open comprehensive analysis pipeline for iTRAQ.	2012	eloped in [C++] and is pr
22467906	r	OCAP: an open comprehensive analysis pipeline for iTRAQ.	2012	ell as an [R package]. the r pa
22451269	r	CpGassoc: an R function for analysis of DNA methylation microarray data.	2012	assoc, an [R package] that can
22426344	mathlab	Proteus: a web-based, context-specific modelling tool for molecular networks.	2012	anguage), [matlab] or fortra
22426344	fortran	Proteus: a web-based, context-specific modelling tool for molecular networks.	2012	matlab or [fortran] format an
22419785	c++	SAMSCOPE: an OpenGL-based real-time interactive scale-free SAM viewer.	2012	mented in [C++] for linux
22419783	java	Harmonization of gene/protein annotations: towards a gold standard MEDLINE.	2012	mented in [java] and its r
22402612	r	rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure.	2012	rehh: an [R package] to detect
22390939	mathlab	Combining multiple approaches for gene microarray classification.	2012	the [mathlab] code of t
22373214	r	Building gene expression profile classifiers with a simple and efficient rejection option in R.	2011	ed in the [R language] and envir
22383736	r	Early immunologic correlates of HIV protection can be identified from computational analysis of complex multivariate T-cell flow cytometry assays.	2012	e through [Bioconductor]. addition
22378710	mathlab	StochSens--Matlab package for sensitivity analysis of stochastic chemical systems.	2012	present a [matlab] package,
22373787	c++	Rchange: algorithms for computing energy changes of RNA secondary structures in response to base mutations.	2012	the [C++] source co
22368255	python	High-quality sequence clustering guided by network topology and multiple alignment likelihood.	2012	the [python] software
22368254	java	SED-ED, a workflow editor for computational biology experiments written in SED-ML.	2012	tandalone [java] applicati
22368248	c++	Unipro UGENE: a unified bioinformatics toolkit.	2012	ritten in [C++] using the
22368246	r	R/DWD: distance-weighted discrimination for classification, visualization and batch adjustment.	2012	able from [CRAN].r-project
22368246	mathlab	R/DWD: distance-weighted discrimination for classification, visualization and batch adjustment.	2012	relied on [matlab], which is
22345622	mathlab	Signal analysis for genome-wide maps of histone modifications measured by ChIP-seq.	2012	e/lpchp a [matlab] implement
22345619	r	GMD: measuring the distance between histograms with applications on high-throughput sequencing reads.	2012	ns) is an [R package] to assess
22333245	r	A method of finding optimal weight factors for compound identification in gas chromatography-mass spectrometry.	2012	sults and [R package] are avail
22332239	java	SBAL: a practical tool to generate and edit structure-based amino acid sequence alignments.	2012	mented in [java] to provid
22330431	r	ICGE: an R package for detecting relevant clusters and atypical units in gene expression.	2012	icge: an [R package] for detec
22321652	r	Identification of polymorphic inversions from genotypes.	2012	a unified [R package] inversion
22308148	javascript	Improving your target-template alignment with MODalign.	2012	html and [javascript] with all
22305354	r	Independent Principal Component Analysis for biologically meaningful dimension reduction of large biological data sets.	2012	ed in the [R package] mixomics
22302572	python	pymzML--Python module for high-throughput bioinformatics on mass spectrometry data.	2012	ension to [python] that offe
22302569	java	ArchTEx: accurate extraction and visualization of next-generation sequence data.	2012	requires [java] 1.6 or ne
22302568	java	Hadoop-BAM: directly manipulating next generation sequencing data in the cloud.	2012	icard sam [jdk], so tools
22292714	r	graphite - a Bioconductor package to convert pathway topology to gene network.	2012	phite - a [Bioconductor] package t
22285827	perl	Chado controller: advanced annotation management with a community annotation system.	2012	resql and [perl].
22262673	python	medpie: an information extraction package for medical message board posts.	2012	[python] 2.6 or 2.
22253290	r	IMA: an R package for high-throughput analysis of Illumina's 450K Infinium methylation data.	2012	ima: an [R package] for high-
22253280	java	BamView: visualizing and interpretation of next-generation sequencing read alignments.	2013	irements: [java] 1.6 or hi
22247280	c++	Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts.	2012	en-source [C++] library s
22247279	r	Robust rank aggregation for gene list integration and meta-analysis.	2012	as a gnu [R package] robustran
22244131	python	PyElph - a software tool for gel images analysis and phylogenetics.	2012	mented in [python] which is
22244038	r	MIPHENO: data normalization for high throughput metabolite analysis.	2012	hrough an [R package] in cran.
22238272	c++	A scalable and portable framework for massively parallel variable selection in genetic association studies.	2012	mented in [C++] and openc
22238261	python	SSuMMo: rapid analysis, comparison and visualization of microbial communities.	2012	en source [python] software,
22238260	perl	PHACTS, a computational approach to classifying the lifestyle of phages.	2012	ed in the [perl] programmi
22219204	perl	NetSeed: a network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment.	2012	tool and [perl] module fo
22210868	java	VarSifter: visualizing and analyzing exome-scale sequence variation data on a desktop computer.	2012	ritten in [java], and is f
22208906	r	Partition decoupling for multi-gene analysis of gene expression profiling data.	2011	sease. an [R package] to carry
25969751	perl	Electric LAMP: Virtual Loop-Mediated Isothermal AMPlification.	2012	elamp, a [perl] script, w
22199382	c++	Modeling mechanistic biological networks: an advanced Boolean approach.	2012	a sample [C++] implement
22199381	r	htSeqTools: high-throughput sequencing quality control, processing and visualization in R.	2012	provide a [Bioconductor] package w
22199380	r	Probe mapping across multiple microarray platforms.	2012	pi and an [R package] to map da
22195644	r	Structural measures for network biology using QuACN.	2011	the [R package] quacn is
22151882	c++	STELLAR: fast and exact local alignments.	2011	the seqan [C++] library v
22177264	r	GC-content normalization for RNA-Seq data.	2011	conductor [R package] edaseq.
22171336	mathlab	MTBindingSim: simulate protein binding to microtubules.	2012	mented in [matlab] and runs
22171334	bash	Detection of microRNAs in color space.	2012	a [bash] shell scr
22171333	java	JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures.	2012	ritten in [java]. it is fr
22171331	r	Identifying small interfering RNA loci from high-throughput sequencing data.	2012	le as the [Bioconductor] (www.bioc
22171329	c++	Transformations for the compression of FASTQ quality scores of next-generation sequencing data.	2012	our [C++] implement
22156367	r	Optimized application of penalized regression methods to diverse genomic data.	2011	he pensim [R package], availabl
22155946	r	GWAtoolbox: an R package for fast quality control and handling of genome-wide association studies meta-analysis data.	2012	olbox: an [R package] for fast
22155870	c++	Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data.	2012	[C++] source co
22155869	perl	Identification and removal of ribosomal RNA sequences from metatranscriptomes.	2012	mented in [perl] and can b
22155866	r	InFiRe -- a novel computational method for the identification of insertion sites in transposon mutagenized bacterial genomes.	2012	ogramming [language r]. for the
22155862	java	Computing graphlet signatures of network nodes and motifs in Cytoscape with GraphletCounter.	2012	mented in [java]. it can b
22151536	r	Empirical comparison of cross-platform normalization methods for gene expression data.	2011	rovide an [R package], conor, c
22136743	r	From hybridization theory to microarray data analysis: performance evaluation.	2011	able from [Bioconductor], which re
22135419	java	DMAN: a Java tool for analysis of multi-well differential scanning fluorimetry experiments.	2012	dman: a [java] tool for
22130594	perl	PGAP: pan-genomes analysis pipeline.	2012	oped with [perl] script on
22121159	r	Modelling time course gene expression data with finite mixtures of linear additive models.	2012	on of the [R package] flexmix i
22121158	c++	Inferring sequence regions under functional divergence in duplicate genes.	2012	rgence. a [C++] program,
22121157	mathlab	CellAnimation: an open source MATLAB framework for microscopy assays.	2012	en source [matlab] framework
22115179	r	iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database.	2011	irefr: an [R package] to manipu
22113085	r	MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation.	2012	ed by the [Bioconductor] project.
22113083	java	A novel and versatile computational tool to model translation.	2012	ritten in [java], and is h
22113082	c++	GenomicTools: a computational platform for developing high-throughput analytics in genomics.	2012	ols and a [C++] api, for
22110245	java	PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs.	2012	spider, a [java] program t
22110244	mathlab	FSR: feature set reduction for scalable and accurate multi-class cancer subtype classification based on copy number.	2012	mented in [matlab] r2010b an
22088846	java	QuRe: software for viral quasispecies reconstruction from next-generation sequencing data.	2012	mented in [java]. it is di
22088841	mathlab	NoRSE: noise reduction and state evaluator for high-frequency single event traces.	2012	-file for [matlab].
22087737	r	ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets.	2011	est files [and R] source co
22085701	mathlab	A flexible framework for sparse simultaneous component based data integration.	2011	ontains a [matlab] implement
22084255	java	PubChem promiscuity: a web resource for gathering compound promiscuity data from PubChem.	2012	. it is a [java] servlet t
22078312	java	Exact score distribution computation for ontological similarity searches.	2011	mented in [java], supports
22072386	java	Wavelet-based image fusion in multi-view three-dimensional microscopy.	2012	eloped in [java]. the soft
22072386	mathlab	Wavelet-based image fusion in multi-view three-dimensional microscopy.	2012	mented in [matlab] (the math
22072385	python	MR-Tandem: parallel X!Tandem using Hadoop MapReduce on Amazon Web Services.	2012	ble and a [python] script th
22072385	c++	MR-Tandem: parallel X!Tandem using Hadoop MapReduce on Amazon Web Services.	2012	x!tandem [C++] executabl
22070167	perl	ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process.	2011	en source [perl] artistic
22059886	c++	A parallel method for enumerating amino acid compositions and masses of all theoretical peptides.	2011	ft visual [C++] and the m
22057162	r	A robust clustering algorithm for identifying problematic samples in genome-wide association studies.	2012	orithm is [written in R] and is fr
22057161	r	Detecting differential binding of transcription factors with ChIP-seq.	2012	[R package] dbchip is
22039209	r	Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data.	2012	an [R package], called c
22039206	c++	RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data.	2012	mented in [C++], the sour
22034839	r	Stepwise classification of cancer samples using clinical and molecular data.	2011	le at the [Bioconductor] website.
22034520	java	SVGMap: configurable image browser for experimental data.	2012	svgmap, a [java] applicati
22034520	javascript	SVGMap: configurable image browser for experimental data.	2012	wser with [javascript] enabled.
22032770	java	Improving ontologies by automatic reasoning and evaluation of logical definitions.	2011	ovide the [java] software
22032230	python	Automated NMR relaxation dispersion data analysis using NESSY.	2011	ritten in [python] for multi
22025481	perl	Graph accordance of next-generation sequence assemblies.	2012	ted in oo [perl] and is av
22025480	r	PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq).	2011	d in perl [and R]. it is fr
22025480	perl	PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq).	2011	mented in [perl] and r. it
21989326	java	A hidden Markov model for copy number variant prediction from whole genome resequencing data.	2011	mented in [java], zinfande
22016409	javascript	VizPrimer: a web server for visualized PCR primer design based on known gene structure.	2011	cture and [javascript] to intera
22016407	java	PRINCIPLE: a tool for associating genes with diseases via network propagation.	2011	iple is a [java] applicati
22014236	r	An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data.	2011	ted as an [R package] called s
22006916	python	Enrich: software for analysis of protein function by enrichment and depletion of variants.	2011	mented in [python] and is av
21999355	r	Comparison of lists of genes based on functional profiles.	2011	able from [Bioconductor], http://b
21995452	r	Bayesian hierarchical clustering for microarray time series data with replicates and outlier measurements.	2011	rt of the [R package] 'bhc' (ve
21984758	mathlab	Sparse distance-based learning for simultaneous multiclass classification and feature selection of metagenomic data.	2011	thod in a [matlab] toolbox c
21961884	javascript	Interactive metagenomic visualization in a Web browser.	2011	html5 and [javascript] implement
21955789	r	Mulcom: a multiple comparison statistical test for microarray data in Bioconductor.	2011	y data in [Bioconductor].
21949271	python	Pybedtools: a flexible Python library for manipulating genomic datasets and annotations.	2011	flexible [python] library f
21937664	r	inSilicoDb: an R/Bioconductor package for accessing human Affymetrix expert-curated datasets from GEO.	2011	ds on the [Bioconductor] project's
21923903	r	Thawing Frozen Robust Multi-array Analysis (fRMA).	2011	resent an [R package], frmatool
21914187	mathlab	MetaboLab--advanced NMR data processing and analysis for metabolomics.	2011	abolab, a [matlab] based sof
21908865	r	Random forest Gini importance favours SNPs with large minor allele frequency: impact, sources and recommendations.	2012	eproduced [using R] code avai
21873638	mathlab	Feature-based 3D motif filtering for ribosomal RNA.	2011	[matlab] code can
21865301	perl	SDRS--an algorithm for analyzing large-scale dose-response data.	2011	able from [CPAN] (www.cpan
21851628	python	DARS-RNP and QUASI-RNP: new statistical potentials for protein-RNA docking.	2011	ructures. [python] implement
21851598	r	Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series.	2011	ble as an [R package] timeshift
21846738	r	Identifying associations between amino acid changes and meta information in alignments.	2011	le on the [CRAN] network a
21846735	python	Reconstructing the architecture of the ancestral amniote genome.	2011	n c++ and [python], is avail
21846735	c++	Reconstructing the architecture of the ancestral amniote genome.	2011	code, in [C++] and pytho
21840874	c++	Conserved and differential gene interactions in dynamical biological systems.	2011	e code in [C++] and r is
21840874	r	Conserved and differential gene interactions in dynamical biological systems.	2011	de in c++ [and R] is availa
21838867	r	IQMNMR: Open source software using time-domain NMR data for automated identification and quantification of metabolites in batches.	2011	qmnmr, an [R package] that inte
21831268	c++	Efficient counting of k-mers in DNA sequences using a bloom filter.	2011	ritten in [C++] and is gp
21828086	r	Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV.	2011	[CRAN] package '
21813478	c++	GlobalMIT: learning globally optimal dynamic bayesian network with the mutual information test criterion.	2011	atlab and [C++], is avail
21813478	mathlab	GlobalMIT: learning globally optimal dynamic bayesian network with the mutual information test criterion.	2011	mented in [matlab] and c++,
21813477	java	The GNAT library for local and remote gene mention normalization.	2011	the gnat [java] library f
21813013	java	RNAexinv: An extended inverse RNA folding from shape and physical attributes to sequences.	2011	teractive [java] applicati
21810900	r	A powerful and flexible approach to the analysis of RNA sequence count data.	2011	an [R package] containin
21804112	r	Penalized regression elucidates aberration hotspots mediating subtype-specific transcriptional responses in breast cancer.	2011	compliant [R package] dance is
21803803	java	JMassBalance: mass-balanced randomization and analysis of metabolic networks.	2011	mented in [java] and freel
21788211	perl	RNAG: a new Gibbs sampler for predicting RNA secondary structure for unaligned sequences.	2011	the [perl] implement
21785131	mathlab	CAM-CM: a signal deconvolution tool for in vivo dynamic contrast-enhanced imaging of complex tissues.	2011	the [matlab] source co
21784795	r	Estimating classification probabilities in high-dimensional diagnostic studies.	2011	urce code [written in R] is freely
21784792	mathlab	GenSSI: a software toolbox for structural identifiability analysis of biological models.	2011	e popular [matlab] environme
21775307	java	Simple high-throughput annotation pipeline (SHAP).	2011	mented in [java], shap rec
21775306	java	GaggleBridge: collaborative data analysis.	2011	ed in the [java] language
21775304	python	Making whole genome multiple alignments usable for biologists.	2011	mented in [python] and has b
21771315	r	Inferring signalling networks from longitudinal data using sampling based approaches in the R-package 'ddepn'.	2011	forge and [CRAN] http://dd
21767381	perl	Bio::Homology::InterologWalk--a Perl module to build putative protein-protein interaction networks through interolog mapping.	2011	ogwalk--a [perl] module to
21765096	python	Stage prediction of embryonic stem cell differentiation from genome-wide expression data.	2011	e form of [python] scripts a
21757464	java	PDBpaint, a visualization webservice to tag protein structures with sequence annotations.	2011	the jmol [java] viewer).
21757464	perl	PDBpaint, a visualization webservice to tag protein structures with sequence annotations.	2011	mented in [perl], with all
21757463	c++	Sufficient statistics and expectation maximization algorithms in phylogenetic tree models.	2011	the [C++] source co
21752800	mathlab	A novel signal processing approach for the detection of copy number variations in the human genome.	2011	tensky/ a [matlab] code for
21742635	c++	DivBayes and SubT: exploring species diversification using Bayesian statistics.	2011	leased as [C++] source co
21742634	r	PREDA: an R-package to identify regional variations in genomic data.	2011	ysis), an [R package] for detec
21737438	mathlab	Simulating systems genetics data with SysGenSIM.	2011	ncoded in [matlab], and a us
21737437	r	APCluster: an R package for affinity propagation clustering.	2011	uster: an [R package] for affin
21727140	python	ModeRNA server: an online tool for modeling RNA 3D structures.	2011	using the [python] language
21724594	python	MethylCoder: software pipeline for bisulfite-treated sequences.	2011	es only a [python] interpret
21714896	r	DOSim: an R package for similarity between diseases based on Disease Ontology.	2011	dosim: an [R package] for simil
21712251	c++	Paired-end RAD-seq for de novo assembly and marker design without available reference.	2011	perl and [C++] implement
21712251	perl	Paired-end RAD-seq for de novo assembly and marker design without available reference.	2011	a [perl] and c++ i
21712248	java	BRISK--research-oriented storage kit for biology-related data.	2011	entation, [java] source co
21697129	java	JSBML: a flexible Java library for working with SBML.	2011	flexible [java] library f
21697128	r	Metab: an R package for high-throughput analysis of metabolomics data generated by GC-MS.	2011	metab: an [R package] for high-
21697127	r	A procedure to statistically evaluate agreement of differential expression for cross-species genomics.	2011	an [R package] is curren
21697126	r	ontoCAT: an R package for ontology traversal and search.	2011	tocat: an [R package] for ontol
21697125	java	GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods.	2011	with its [java] source co
21693065	r	Sparse PLS discriminant analysis: biologically relevant feature selection and graphical displays for multiclass problems.	2011	le in the [R package] mixomics,
21693013	r	Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data.	2011	able in a [Bioconductor] package '
21689434	java	PhyloMap: an algorithm for visualizing relationships of large sequence data sets and its application to the influenza A virus genome.	2011	mented in [java], and the
21685105	r	vipR: variant identification in pooled DNA using R.	2011	ooled dna [using R].
21685095	java	Small sets of interacting proteins suggest functional linkage mechanisms via Bayesian analogical reasoning.	2011	[java] code is a
21685094	r	From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems.	2011	d into an [R package] and tied
21685091	mathlab	ccSVM: correcting Support Vector Machines for confounding factors in biological data classification.	2011	tation in [matlab] is availa
21685088	c++	StructHDP: automatic inference of number of clusters and population structure from admixed genotype data.	2011	ritten in [C++]. the code
21685086	python	An enhanced Petri-net model to predict synergistic effects of pairwise drug combinations from gene microarray data.	2011	mented in [python] 2.7 progr
21685084	java	A generalized model for multi-marker analysis of cell cycle progression in synchrony experiments.	2011	cell. the [java] implement
21685055	r	Menu-driven cloud computing and resource sharing for R and Bioconductor.	2011	ring data [and R] scripts w
21685053	python	CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer.	2011	source in [python] and c++.
21685053	c++	CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer.	2011	ython and [C++]. requires
21685051	python	Methyl-Analyzer--whole genome DNA methylation profiling.	2011	yzer is a [python] package t
21685046	r	Noise reduction in genome-wide perturbation screens using linear mixed-effect models.	2011	.org. the [R package] htsmix is
21682923	r	MLPAstats: an R GUI package for the integrated analysis of copy number alterations using MLPA data.	2011	stats, an [R package] designed
21666268	java	MGV: a generic graph viewer for comparative omics data.	2011	mented in [java] and freel
21666267	java	Xwalk: computing and visualizing distances in cross-linking experiments.	2011	and-alone [java] applicati
21666266	r	Parent-specific copy number in paired tumor-normal studies using circular binary segmentation.	2011	en-source [R package] named psc
21666252	java	Letter to the editor: SeqXML and OrthoXML: standards for sequence and orthology information.	2011	tions for [biojava], bioperl,
21666252	python	Letter to the editor: SeqXML and OrthoXML: standards for sequence and orthology information.	2011	perl, and [biopython]. orthoxml
21666252	perl	Letter to the editor: SeqXML and OrthoXML: standards for sequence and orthology information.	2011	biojava, [bioperl], and biop
21659319	r	mapDamage: testing for damage patterns in ancient DNA sequences.	2011	ols suite [and R] environme
21659319	perl	mapDamage: testing for damage patterns in ancient DNA sequences.	2011	mage is a [perl] script th
21653523	java	The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways.	2011	mented in [java] and suppo
21653522	perl	The variant call format and VCFtools.	2011	a general [perl] api.
21636591	java	PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs).	2011	tions and [java] source co
21622663	perl	Computational discovery of human coding and non-coding transcripts with conserved splice sites.	2011	er with a [perl] implement
21619703	java	OntoCAT--simple ontology search and integration in Java, R and REST/JavaScript.	2011	ration in [java], r and re
21619662	c++	miRFam: an effective automatic miRNA classification method based on n-grams and a multiclass SVM.	2011	ritten in [C++], is freel
21615972	c++	MixtureTree: a program for constructing phylogeny.	2011	ritten in [C++] is a linu
21615941	mathlab	Fast empirical Bayesian LASSO for multiple quantitative trait locus mapping.	2011	mented in [matlab] had simil
21615941	fortran	Fast empirical Bayesian LASSO for multiple quantitative trait locus mapping.	2011	mented in [fortran], and that
21612622	r	rnaSeqMap: a Bioconductor package for RNA sequencing data exploration.	2011	seqmap: a [Bioconductor] package f
21599881	c++	TreeRipper web application: towards a fully automated optical tree recognition software.	2011	mand line [C++] program f
21596792	c++	linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type.	2011	ritten in [C++] and desig
21596792	r	linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type.	2011	kcomm: an [R package] for the g
21596789	java	GenPlay, a multipurpose genome analyzer and browser.	2011	ritten in [java] and runs
21595965	javascript	Web-based metabolic network visualization with a zooming user interface.	2011	ritten in [javascript] for the c
21595880	r	Genotype calling in tetraploid species from bi-allelic marker data using mixture models.	2011	ed in the [R package] fittetra,
21593133	mathlab	An ensemble biclustering approach for querying gene expression compendia with experimental lists.	2011	compiled [matlab] code is a
21593132	java	Java bioinformatics analysis web services for multiple sequence alignment--JABAWS:MSA.	2011	[java] bioinform
21586520	java	Genome-wide association studies pipeline (GWASpi): a desktop application for genome-wide SNP analysis and management.	2011	mented in [java], apache-d
21586517	perl	Hidden conformations in protein structures.	2011	a [perl] script im
21561920	r	Model-based gene set analysis for Bioconductor.	2011	rs of the [R language]. our pack
21554689	r	Elastic SCAD as a novel penalization method for SVM classification tasks in high-dimensional data.	2011	available [R package] 'penalize
21551149	c++	An MCMC algorithm for detecting short adjacent repeats shared by multiple sequences.	2011	e related [C++] source co
21551147	mathlab	The role of indirect connections in gene networks in predicting function.	2011	ovided in [matlab] m-code.
21551146	c++	Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing.	2011	ten in c, [C++] and perl
21551146	c	Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing.	2011	leaff are [written in C], c++ and
21551146	perl	Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing.	2011	, c++ and [perl] for linux
21551143	c++	A multiple network learning approach to capture system-wide condition-specific responses.	2011	[C++] code can
21551136	python	BINOCh: binding inference from nucleosome occupancy changes.	2011	en source [python] package i
21548938	r	ArrayInitiative - a tool that simplifies creating custom Affymetrix CDFs.	2011	ilable in [Bioconductor].
21546399	r	Clonality: an R package for testing clonal relatedness of two tumors from the same patient based on their genomic profiles.	2011	ality: an [R package] for testi
21546396	java	famCNV: copy number variant association for quantitative traits in families.	2011	the [java] package i
21546394	java	ReMark: an automatic program for clustering orthologs flexibly combining a Recursive and a Markov clustering algorithms.	2011	mented in [java] 1.6 and s
21546390	mathlab	Multiple-rule bias in the comparison of classification rules.	2011	mented in [matlab]. the sour
21535899	perl	An automated homology-based approach for identifying transposable elements.	2011	numerous [bioperl] scripts.
21535878	java	SNPPicker: high quality tag SNP selection across multiple populations.	2011	scripts, [java] source co
21535878	perl	SNPPicker: high quality tag SNP selection across multiple populations.	2011	runtime. [perl] scripts,
21531770	r	parmigene--a parallel R package for mutual information estimation and gene network reconstruction.	2011	parallel [R package] for mutua
21531769	c++	A detailed investigation of accessibilities around target sites of siRNAs and miRNAs.	2011	the [C++] source co
21527044	r	Sequential interim analyses of survival data in DNA microarray experiments.	2011	as a new [R package] 'survgene
21527030	python	STSE: Spatio-Temporal Simulation Environment Dedicated to Biology.	2011	org/. the [python] source co
21521499	python	ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data.	2011	d in c++, [python], and perl
21521499	c++	ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data.	2011	mented in [C++], python,
21521499	perl	ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data.	2011	thon, and [perl] and has b
21513508	java	The proteogenomic mapping tool.	2011	ncludes a [java] implement
21511716	java	Exploiting prior knowledge and gene distances in the analysis of tumor expression profiles with extended Hidden Markov Models.	2011	en-source [java] library j
21511714	java	CytoModeler: a tool for bridging large-scale network analysis and dynamic quantitative modeling.	2011	en-source [java] applicati
21489225	c++	Processing SPARQL queries with regular expressions in RDF databases.	2011	mework in [C++] and condu
21505037	python	A graphical interface for the FoldX forcefield.	2011	ritten in [python] and is fr
21505033	c++	Rgtsp: a generalized top scoring pairs package for class prediction.	2011	full [C++] source co
21505033	r	Rgtsp: a generalized top scoring pairs package for class prediction.	2011	code and [R package] rgtsp are
21504561	r	PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment.	2011	volution, [written in R], using th
21501497	java	Multithreaded comparative RNA secondary structure prediction using stochastic context-free grammars.	2011	table and [java] source co
21501495	python	Screening synteny blocks in pairwise genome comparisons through integer programming.	2011	izations. [python] codes and
21501472	r	SAQC: SNP array quality control.	2011	ftware is [written in R] and r-gui
21498550	r	Exon array data analysis using Affymetrix power tools and R statistical software.	2011	wer tools [and R] statistic
21498403	perl	PathScan: a tool for discerning mutational significance in groups of putative cancer genes.	2011	mented in [perl] and is av
21498400	java	BACOM: in silico detection of genomic deletion types and correction of normal cell contamination in copy number data.	2011	en-source [java] applicati
21498399	r	Normalizing bead-based microRNA expression data: a measurement error model-based approach.	2011	asets and [R package] are avail
21498398	r	OTUbase: an R infrastructure package for operational taxonomic unit data.	2011	ase is an [R package] designed
21496265	java	SNP-based pathway enrichment analysis for genome-wide association studies.	2011	thod in a [java] software
21493657	java	'Sciencenet'--towards a global search and share engine for all scientific knowledge.	2011	based on [java] 1.6.
21493657	python	'Sciencenet'--towards a global search and share engine for all scientific knowledge.	2011	ritten in [python] 2.7, and
21493652	c++	BamTools: a C++ API and toolkit for analyzing and managing BAM files.	2011	mtools: a [C++] api and t
21486937	java	Cobweb: a Java applet for network exploration and visualisation.	2011	cobweb: a [java] applet fo
21478488	python	Reliability-oriented bioinformatic networks visualization.	2011	n c++ and [python], and cons
21478488	c++	Reliability-oriented bioinformatic networks visualization.	2011	ritten in [C++] and pytho
21478487	c++	Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data.	2011	a [C++] and perl
21478487	perl	Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data.	2011	a c++ and [perl] implement
21471018	r	Multi-platform segmentation for joint detection of copy number variants.	2011	ted in an [R package] mpss, and
21471012	python	ProDy: protein dynamics inferred from theory and experiments.	2011	veloped a [python] package,
21471010	r	Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies.	2011	from www.[CRAN].r-project
21450717	r	A qualitative continuous model of cellular auxin and brassinosteroid signaling and their crosstalk.	2011	e via the [Bioconductor] repositor
21450711	r	pathClass: an R-package for integration of pathway knowledge into support vector machines for biomarker discovery.	2011	ge on the [CRAN] repositor
21447171	c++	DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI.	2011	n in cuda [C++] and mpi.
21422072	r	anota: Analysis of differential translation in genome-wide studies.	2011	the anota [Bioconductor] package,
21414990	r	AStream: an R package for annotating LC/MS metabolomic data.	2011	tream: an [R package] for annot
21414234	java	ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry.	2011	ension of [java] algorithm
21414208	r	pROC: an open-source package for R and S+ to analyze and compare ROC curves.	2011	rough the [CRAN] and csan
21398675	c++	fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios.	2011	coal is a [C++] program c
21398674	r	TEQC: an R package for quality control in target capture experiments.	2011	teqc: an [R package] for quali
21398673	r	PRIMe: a method for characterization and evaluation of pleiotropic regions from multiple genome-wide association studies.	2011	the perl [and R] scripts a
21398673	perl	PRIMe: a method for characterization and evaluation of pleiotropic regions from multiple genome-wide association studies.	2011	the [perl] and r scr
21398670	r	Identification and quantification of metabolites in (1)H NMR spectra by Bayesian model selection.	2011	the [R package] bquant is
21398667	c++	GeCo++: a C++ library for genomic features computation and annotation in the presence of variants.	2011	geco++: a [C++] library f
21388547	c++	The dChip survival analysis module for microarray data.	2011	in visual [C++] also enab
21385435	java	compomics-utilities: an open-source Java library for computational proteomics.	2011	en-source [java] library f
21372081	mathlab	Mixtures of common t-factor analyzers for clustering high-dimensional microarray data.	2011	mented in [matlab]. the matl
21342585	c++	Repeat-aware modeling and correction of short read errors.	2011	mented in [C++] and is fr
21342575	python	HDX-analyzer: a novel package for statistical analysis of protein structure dynamics.	2011	using r, [python], and rpy2
21342575	r	HDX-analyzer: a novel package for statistical analysis of protein structure dynamics.	2011	etry data [using R], python,
21367873	r	SurvJamda: an R package to predict patients' survival and risk assessment using joint analysis of microarray gene expression data.	2011	jamda: an [R package] to predic
21367872	java	Human variation database: an open-source database template for genomic discovery.	2011	-platform [java] api is pr
21357575	mathlab	STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB.	2011	box 2 for [matlab].
21357574	r	aCGH.Spline--an R package for aCGH dye bias normalization.	2011	pline--an [R package] for acgh
21352572	perl	BIO::Phylo-phyloinformatic analysis using perl.	2011	sis using [perl].
21352538	python	A lightweight, flow-based toolkit for parallel and distributed bioinformatics pipelines.	2011	elines in [python] ('papy').
21349873	java	AGRA: analysis of gene ranking algorithms.	2011	mented in [java] and runni
21349869	r	R453Plus1Toolbox: an R/Bioconductor package for analyzing Roche 454 Sequencing data.	2011	ttp://www.[Bioconductor].org/. a v
21349867	java	Interactive, multiscale navigation of large and complicated biological networks.	2011	[java] implement
21335612	c++	fconv: Format conversion, manipulation and feature computation of molecular data.	2011	license. [C++] sources a
21330291	c++	libfbi: a C++ implementation for fast box intersection and application to sparse mass spectrometry data.	2011	libfbi: a [C++] implement
21330289	r	Defining an informativeness metric for clustering gene expression data.	2011	conductor [R package] attract;
21330288	python	Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs.	2011	a c++ and [python] implement
21330288	c++	Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs.	2011	a [C++] and pytho
21325302	python	Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows.	2011	in ruby, [python] and php.
21317143	r	Cross-platform comparison of microarray data using order restricted inference.	2011	nted in c [and R] is availa
21310747	c++	Entropy-accelerated exact clustering of protein decoys.	2011	our [C++] software
21310746	mathlab	FISH Finder: a high-throughput tool for analyzing FISH images.	2011	tandalone [matlab] applicati
21300702	r	tigre: Transcription factor inference through gaussian process reconstruction of expression for bioconductor.	2011	ssion for [Bioconductor].
21300701	c++	HLA*IMP--an integrated framework for imputing classical HLA alleles from SNP genotypes.	2011	mented in [C++] and perl,
21300701	perl	HLA*IMP--an integrated framework for imputing classical HLA alleles from SNP genotypes.	2011	n c++ and [perl], is avail
21296754	c++	SpaCEM3: a software for biological module detection when data is incomplete, high dimensional and dependent.	2011	eloped in [C++] and can b
21296752	java	DDN: a caBIG® analytical tool for differential network analysis.	2011	tandalone [java] applicati
21296752	mathlab	DDN: a caBIG® analytical tool for differential network analysis.	2011	java and [matlab] source co
21296750	c++	SIMA: simultaneous multiple alignment of LC/MS peak lists.	2011	a [C++] implement
21296749	mathlab	LSPR: an integrated periodicity detection algorithm for unevenly sampled temporal microarray data.	2011	mented as [matlab] software
21296748	javascript	Gobe: an interactive, web-based tool for comparative genomic visualization.	2011	heets and [javascript] callback
21278367	python	Easyfig: a genome comparison visualizer.	2011	yfig is a [python] applicati
21278191	java	Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format.	2011	dependent [java] and avail
21278190	perl	A Ruby API to query the Ensembl database for genomic features.	2011	through a [perl] api for a
21278188	java	PiNGO: a Cytoscape plugin to find candidate genes in biological networks.	2011	en-source [java] package u
21278185	perl	Quality control and preprocessing of metagenomic datasets.	2011	mented in [perl] and can b
21269502	r	VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R.	2011	agram, an [R package] that enab
21266444	python	Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions.	2011	a [python] package i
21261974	java	PileLine: a toolbox to handle genome position information in next-generation sequencing studies.	2011	coded in [java] and run o
21258065	mathlab	Computational refinement of post-translational modifications predicted from tandem mass spectrometry.	2011	mented in [matlab] and is fr
21258062	r	HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens.	2011	en in the [R language] and freel
21258060	perl	WIST: toolkit for rapid, customized LIMS development.	2011	mented in [perl] and may b
21245054	r	BayesPeak--an R package for analysing ChIP-seq data.	2011	speak--an [R package] for analy
21245051	c++	Automated bond order assignment as an optimization problem.	2011	en-source [C++] lgpl libr
21210988	java	The Musite open-source framework for phosphorylation-site prediction.	2010	-designed [java] applicati
21210987	perl	ONTO-ToolKit: enabling bio-ontology engineering via Galaxy.	2010	ended the [perl] suite ont
21210979	java	The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button.	2010	e of sql, [java], r, or ht
21210978	python	An intuitive Python interface for Bioconductor libraries demonstrates the utility of language translators.	2010	intuitive [python] interface
21210978	r	An intuitive Python interface for Bioconductor libraries demonstrates the utility of language translators.	2010	ed on the [R language], has beco
21210977	python	interPopula: a Python API to access the HapMap Project dataset.	2010	popula: a [python] api to ac
21233169	c++	Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering.	2011	mented in [C++] and suppo
21233168	r	High-accuracy prediction of bacterial type III secreted effectors based on position-specific amino acid composition profiles.	2011	an [R package] of bpbaac
21233166	r	A pipeline for RNA-seq data processing and quality assessment.	2011	the [R package] is availa
21233165	c++	ESS++: a C++ objected-oriented algorithm for Bayesian stochastic search model exploration.	2011	ess++: a [C++] objected-
21228048	r	CNAmet: an R package for integrating copy number, methylation and expression data.	2011	namet: an [R package] for integ
21224286	python	GPU accelerated biochemical network simulation.	2011	present a [python] package,
21217123	r	Robust linear regression methods in association studies.	2011	from the [R package] kinship i
21217122	c++	A fast, lock-free approach for efficient parallel counting of occurrences of k-mers.	2011	ritten in [C++] and is gp
21216779	java	A Java API for working with PubChem datasets.	2011	a [java] api for w
21216776	java	MADGene: retrieval and processing of gene identifier lists for the analysis of heterogeneous microarray datasets.	2011	ase and a [java] applicati
21216773	java	A method for identifying haplotypes carrying the causative allele in positive natural selection and genome-wide association studies.	2011	a [java] program,
21208987	r	flowPhyto: enabling automated analysis of microscopic algae from continuous flow cytometric data.	2011	phyto, an [R package] that perf
21208986	java	MIRACH: efficient model checker for quantitative biological pathway models.	2011	ped using [java] and thus
21208982	java	Tabix: fast retrieval of sequence features from generic TAB-delimited files.	2011	ary in c, [java], perl and
21208982	python	Tabix: fast retrieval of sequence features from generic TAB-delimited files.	2011	perl and [python]. it is pa
21208982	perl	Tabix: fast retrieval of sequence features from generic TAB-delimited files.	2011	c, java, [perl] and pytho
21199577	r	MTML-msBayes: approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity.	2011	f perl, c [and R] programs
21199577	perl	MTML-msBayes: approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity.	2011	isting of [perl], c and r
21193521	c++	Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences.	2011	d in ansi [C++] and can b
21177328	mathlab	Improvements in the reconstruction of time-varying gene regulatory networks: dynamic programming and regularization by information sharing among genes.	2011	a [matlab] implement
21172910	mathlab	Functional integration of a metabolic network model and expression data without arbitrary thresholding.	2011	mented in [matlab] and requi
21169379	java	Lipid Data Analyzer: unattended identification and quantitation of lipids in LC-MS data.	2011	the [java] applicati
21169378	r	phangorn: phylogenetic analysis in R.	2011	is in the [R language]. previous
21169377	c++	ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping.	2011	ritten in [C++] and perl.
21169377	perl	ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping.	2011	n c++ and [perl]. it runs
21159624	r	Automated analysis of information processing, kinetic independence and modular architecture in biochemical networks using MIDIA.	2011	xtensible [R package] that perf
21149343	perl	When the Web meets the cell: using personalized PageRank for analyzing protein interaction networks.	2011	the [perl] script fo
21149340	java	Cytoscape 2.8: new features for data integration and network visualization.	2011	a desktop [java] applicati
21149278	c++	Exploring metabolic pathways in genome-scale networks via generating flux modes.	2011	e code in [C++] is availa
21148545	c++	SurreyFBA: a command line tool and graphics user interface for constraint-based modeling of genome-scale metabolic reaction networks.	2011	mented in [C++], is easil
21148542	c++	SlideSort: all pairs similarity search for short reads.	2011	files and [C++] libraries
21134892	r	Rseg--an R package to optimize segmentation of SNP array data.	2011	rseg--an [R package] to optimi
21134890	r	Predicting in vitro drug sensitivity using Random Forests.	2011	en in the [R language] and will
21129181	r	Merged consensus clustering to assess and improve class discovery with microarray data.	2010	scribe an [R package] containin
21127034	mathlab	A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain-peptide interaction from primary sequence.	2011	the [matlab] code for
21127032	c++	MTR: taxonomic annotation of short metagenomic reads using clustering at multiple taxonomic ranks.	2011	atlab and [C++] source co
21127032	mathlab	MTR: taxonomic annotation of short metagenomic reads using clustering at multiple taxonomic ranks.	2011	[matlab] and c++ s
21123224	java	GLay: community structure analysis of biological networks.	2010	cytoscape [java] program,
21118823	python	Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution.	2011	[python] code for
21118515	mathlab	Knowledge-based matrix factorization temporally resolves the cellular responses to IL-6 stimulation.	2010	ethods. a [matlab] implement
21118506	r	Preprocessing of gene expression data by optimally robust estimators.	2010	ed in the [R package] named rob
21115438	java	Real-world comparison of CPU and GPU implementations of SNPrank: a network analysis tool for GWAS.	2011	atlab and [java] as well a
21115438	python	Real-world comparison of CPU and GPU implementations of SNPrank: a network analysis tool for GWAS.	2011	including [python], matlab a
21115438	mathlab	Real-world comparison of CPU and GPU implementations of SNPrank: a network analysis tool for GWAS.	2011	g python, [matlab] and java
21115436	mathlab	von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models.	2011	-platform [matlab] extension
21092255	java	Reticular alignment: a progressive corner-cutting method for multiple sequence alignment.	2010	am in the [java] programmi
21088029	r	Efficient change point detection for genomic sequences of continuous measurements.	2011	n the new [R package] cumseg av
21081511	python	GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments.	2011	mented in [python] and runs
21076148	perl	PLEXY: efficient target prediction for box C/D snoRNAs.	2011	the [perl] script pl
21075747	r	QuACN: an R package for analyzing complex biological networks quantitatively.	2011	quacn: an [R package] for analy
21075742	r	Inference of gene networks--application to Bifidobacterium.	2011	le at www.[Bioconductor].org and a
21073736	r	Quantification and deconvolution of asymmetric LC-MS peaks using the bi-Gaussian mixture model and statistical model selection.	2010	ed in the [R package] aplcms: h
21062762	mathlab	Inverse perturbation for optimal intervention in gene regulatory networks.	2011	the [matlab] code for
21044358	r	Stromal microenvironment processes unveiled by biological component analysis of gene expression in xenograft tumor models.	2010	yb probes [and R] script ar
21050468	r	Optimizing transformations for automated, high throughput analysis of flow cytometry data.	2010	ithin the [Bioconductor] flowcore
21045073	r	dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks.	2011	hod in an [R package], which ca
21037244	java	Bayesian sampling of genomic rearrangement scenarios via double cut and join.	2010	mented in [java] 1.5 progr
21034480	mathlab	Predicting domain-domain interaction based on domain profiles with feature selection and support vector machines.	2010	mented in [matlab] and suppo
20980271	mathlab	Optimized data fusion for K-means Laplacian clustering.	2011	the [matlab] code of a
20973958	c++	BALL--biochemical algorithms library 1.3.	2010	extensive [C++] class lib
20971988	perl	The GMOD Drupal bioinformatic server framework.	2010	n php and [perl]. freely a
20971985	r	Generalized random set framework for functional enrichment analysis using primary genomics datasets.	2011	rt of the [R package] clean fro
20966004	r	R/qtl: high-throughput multiple QTL mapping.	2010	atistical [language r], and is m
20946609	perl	Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize.	2010	rver, and [perl] cgi scrip
20946604	perl	A framework for automated enrichment of functionally significant inverted repeats in whole genomes.	2010	rience in [perl].
20946598	perl	Next generation models for storage and representation of microbial biological annotation.	2010	esources, [perl], c, and u
20959382	java	MiRonTop: mining microRNAs targets across large scale gene expression studies.	2010	an online [java] web tool
20958996	mathlab	Discover protein complexes in protein-protein interaction networks using parametric local modularity.	2010	mented in [matlab] and is fr
20956245	perl	High-quality annotation of promoter regions for 913 bacterial genomes.	2010	mented in [perl] and suppo
20956244	java	Interactive microbial genome visualization with GView.	2010	view is a [java] applicati
20956243	c++	SPLATCHE2: a spatially explicit simulation framework for complex demography, genetic admixture and recombination.	2010	che2 is a [C++] program c
20950483	mathlab	Accurate peak list extraction from proteomic mass spectra for identification and profiling studies.	2010	ssspec, a [matlab] implement
20947524	java	OmicsAnalyzer: a Cytoscape plug-in suite for modeling omics data.	2010	mented in [java], omicsana
20947523	java	The SMARTCyp cytochrome P450 metabolism prediction server.	2010	smartcyp [java] program a
20942945	mathlab	Quadratic variance models for adaptively preprocessing SELDI-TOF mass spectrometry data.	2010	mented in [matlab]. the prop
20942913	java	Confronting two-pair primer design for enzyme-free SNP genotyping based on a genetic algorithm.	2010	mented in [java] and a use
20937596	java	Pre-calculated protein structure alignments at the RCSB PDB website.	2010	ttp://www.[biojava].org. a so
20929913	mathlab	R3D Align: global pairwise alignment of RNA 3D structures using local superpositions.	2010	lign. the [matlab] source co
20929911	python	PyETV: a PyMOL evolutionary trace viewer to analyze functional site predictions in protein complexes.	2010	ritten in [python]. installa
20926422	perl	TURNIP: tracking unresolved nucleotide polymorphisms in large hard-to-assemble regions of repetitive DNA sequence.	2010	suite of [perl] scripts a
20926421	python	MEDELLER: homology-based coordinate generation for membrane proteins.	2010	mented in [python], bash and
20926421	bash	MEDELLER: homology-based coordinate generation for membrane proteins.	2010	n python, [bash] and perl
20926421	perl	MEDELLER: homology-based coordinate generation for membrane proteins.	2010	bash and [perl] cgi for u
20926419	java	GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop.	2010	mented in [java] and is fr
20880956	r	A statistical framework for Illumina DNA methylation arrays.	2010	[R package] lumiwclus
20871108	java	SylArray: a web server for automated detection of miRNA effects from expression data.	2010	perl and [java] and also
20871108	perl	SylArray: a web server for automated detection of miRNA effects from expression data.	2010	perl-cgi, [perl] and java
20861030	r	Girafe--an R/Bioconductor package for functional exploration of aligned next-generation sequencing reads.	2010	the [R package] girafe is
20861029	java	FastPval: a fast and memory efficient program to calculate very low P-values from empirical distribution.	2010	file, the [java] gui and s
20861028	c++	BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis.	2010	ucky is a [C++] program t
20847220	java	Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape.	2010	with sun [java] 1.5 or la
20847218	python	Ruffus: a lightweight Python library for computational pipelines.	2010	ghtweight [python] library f
20843356	perl	Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions.	2010	ritten in [perl].
20837570	perl	A unified index of sequence quality and contig overlap for DNA barcoding.	2010	a gpl [perl] script is
20834038	r	Semi-supervised recursively partitioned mixture models for identifying cancer subtypes.	2010	rried out [using R] (http://w
20834037	c++	Reptile: representative tiling for short read error correction.	2010	mented in [C++] and is av
20829444	java	The Chemical Translation Service--a web-based tool to improve standardization of metabolomic reports.	2010	roovy and [java], the web
20828413	r	Multivariate Hawkes process models of the occurrence of regulatory elements.	2010	ble as an [R package] from http
20828407	java	Next generation tools for genomic data generation, distribution, and visualization.	2010	tandalone [java] swing app
20823315	mathlab	De-correlating expression in gene-set analysis.	2010	the [matlab] codes and
20823308	c++	RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming.	2010	mented in [C++], and the
20823304	mathlab	Integrating genome assemblies with MAIA.	2010	able as a [matlab] package a
20823298	mathlab	Automated construction and analysis of the design space for biochemical systems.	2010	olbox for [matlab] is freely
20817744	mathlab	Using manifold embedding for assessing and predicting protein interactions from high-throughput experimental data.	2010	[matlab] code impl
20815925	c++	Harvest: an open-source tool for the validation and improvement of peptide identification metrics and fragmentation exploration.	2010	mework in [C++] for analy
20813878	mathlab	Global modeling of transcriptional responses in interaction networks.	2010	in r and [matlab] at http:/
20810601	c++	CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data.	2010	en source [C++] code buil
20810601	r	CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data.	2010	the [R package] cogaps an
20801914	r	DCGL: an R package for identifying differentially coexpressed genes and links from gene expression microarray data.	2010	dcgl: an [R package] for ident
20739311	mathlab	TFInfer: a tool for probabilistic inference of transcription factor activities.	2010	n earlier [matlab] version,
20739307	java	BioRuby: bioinformatics software for the Ruby programming language.	2010	ns on the [java] virtual m
20736340	java	Deep and wide digging for binding motifs in ChIP-Seq data.	2010	_genetika [java] package:
20733064	c++	Improving performances of suboptimal greedy iterative biclustering heuristics via localization.	2010	s in leda [C++] library,
20733063	python	OpenStructure: a flexible software framework for computational structural biology.	2010	+ or in a [python] layer, me
20733063	c++	OpenStructure: a flexible software framework for computational structural biology.	2010	ritten in [C++] with a cl
20709689	java	QuantProReloaded: quantitative analysis of microspot immunoassays.	2010	in r and [java] and is op
20709689	r	QuantProReloaded: quantitative analysis of microspot immunoassays.	2010	loaded is [written in R] and java
20704747	perl	TF-finder: a software package for identifying transcription factors involved in biological processes using microarray data and existing knowledge base.	2010	ascca, a [perl] controlle
20702402	java	Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies.	2010	abase and [java] applicati
20702399	mathlab	Automated analysis of time-lapse fluorescence microscopy images: from live cell images to intracellular foci.	2010	mented in [matlab] (the math
20702396	mathlab	Cross-species queries of large gene expression databases.	2010	lts and a [matlab] implement
20702395	java	BDVal: reproducible large-scale predictive model development and validation in high-throughput datasets.	2010	mented in [java], provided
20702394	python	RBSDesigner: software for designing synthetic ribosome binding sites that yields a desired level of protein expression.	2010	ritten in [python] and micro
20696734	perl	MASiVE: Mapping and Analysis of Sirevirus Elements in plant genome sequences.	2010	[perl] source co
20691053	java	PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci.	2010	n c++ and [java] is provid
20691053	c++	PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci.	2010	e code in [C++] and java
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20673335	java	OpenChrom: a cross-platform open source software for the mass spectrometric analysis of chromatographic data.	2010	ritten in [java]. openchro
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20634205	r	RPPanalyzer: Analysis of reverse-phase protein array data.	2010	ge on the [CRAN] platform
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20591907	python	ABC-SysBio--approximate Bayesian computation in Python with GPU support.	2010	tation in [python] with gpu
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20576626	r	Single feature polymorphism detection using recombinant inbred line microarray expression data.	2010	the [R package] 'dipsfp'
20576622	r	Cassis: detection of genomic rearrangement breakpoints.	2010	perl [and R] scripts a
20576622	perl	Cassis: detection of genomic rearrangement breakpoints.	2010	[perl] and r scr
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20562450	c	Bridges: a tool for identifying local similarities in long sequences.	2010	ed in the [C programming] language
20562416	python	Manipulation of FASTQ data with Galaxy.	2010	mented in [python] and has b
20562414	java	Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels.	2010	ed in the [java] language
20554691	mathlab	Causal relationship inference for a large-scale cellular network.	2010	the [matlab] files for
20554688	c++	A Bayesian approach using covariance of single nucleotide polymorphism data to detect differences in linkage disequilibrium patterns between groups of individuals.	2010	ferences) [C++] software,
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20551134	java	Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood.	2010	and-alone [java] applicati
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20546611	java	Accessing the SEED genome databases via Web services API: tools for programmers.	2010	thon, and [java].
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20546611	perl	Accessing the SEED genome databases via Web services API: tools for programmers.	2010	s such as [perl], python,
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20529941	python	Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph.	2010	en in the [python] programmi
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20529902	python	Analyzing circadian expression data by harmonic regression based on autoregressive spectral estimation.	2010	mented by [python] and r. al
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20529900	mathlab	Inferring combinatorial association logic networks in multimodal genome-wide screens.	2010	the [matlab] code of t
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20529363	mathlab	L2-norm multiple kernel learning and its application to biomedical data fusion.	2010	the [matlab] code of a
20525223	mathlab	poolMC: smart pooling of mRNA samples in microarray experiments.	2010	eloped in [matlab]. a proof-
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20519286	mathlab	Structure-based variable selection for survival data.	2010	[matlab] and r cod
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20511363	java	geWorkbench: an open source platform for integrative genomics.	2010	en source [java] desktop a
20509870	python	Colonyzer: automated quantification of micro-organism growth characteristics on solid agar.	2010	packages: [python], rpy and
20505005	java	A UIMA wrapper for the NCBO annotator.	2010	mented in [java] for suppo
20505002	perl	Threshold Average Precision (TAP-k): a measure of retrieval designed for bioinformatics.	2010	nloadable [perl] script ar
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20501552	c	A parallel algorithm to compute chemical organizations in biological networks.	2010	standard [C programming] language
20492697	java	A high-level 3D visualization API for Java and ImageJ.	2010	n api for [java] and image
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20472542	python	The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell.	2010	rce code, [python] bindings
20472541	perl	Classification of DNA sequences using Bloom filters.	2010	aster 1.6 [perl] module ca
20472540	java	Interactive software tool to comprehend the calculation of optimal sequence alignments with dynamic programming.	2010	en in the [java] computer
20462443	mathlab	A comparison of approximation techniques for variance-based sensitivity analysis of biochemical reaction systems.	2010	coded in [matlab], which im
20462408	r	TumorBoost: normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays.	2010	-platform [R package] aroma.cn,
20459813	perl	eHive: an artificial intelligence workflow system for genomic analysis.	2010	agent, a [perl] script, q
20459804	r	ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data.	2010	akanno: a [Bioconductor] package t
20459647	r	Odefy--from discrete to continuous models.	2010	box, sbml [and R] script fi
20459647	mathlab	Odefy--from discrete to continuous models.	2010	uad, gna, [matlab] script fi
20457667	r	Repitools: an R package for the analysis of enrichment-based epigenomic data.	2010	tools: an [R package] for the a
20453004	mathlab	Discover regulatory DNA elements using chromatin signatures and artificial neural network.	2010	mented in [matlab]. the sour
20453003	c++	Arcadia: a visualization tool for metabolic pathways.	2010	ritten in [C++]. the sour
20439257	c++	A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches.	2010	[C++] source co
20439256	c++	Deuteration distribution estimation with improved sequence coverage for HX/MS experiments.	2010	mented in [C++] and inclu
20438641	python	Partitioning of copy-number genotypes in pedigrees.	2010	with the [python] interpret
20435580	python	The Genomedata format for storing large-scale functional genomics data.	2010	tation in [python] and c com
20429928	c++	WaveletQuant, an improved quantification software based on wavelet signal threshold de-noising for labeled quantitative proteomic analysis.	2010	ng visual [C++] 2005 expr
20427518	r	ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking.	2010	software, [written in R], under gp
20427516	python	Modeling RNA loops using sequence homology and geometric constraints.	2010	mented in [python], mysql an
20421198	python	DendroPy: a Python library for phylogenetic computing.	2010	ndropy: a [python] library f
20418341	r	CGHnormaliter: a Bioconductor package for normalization of array CGH data with many CNAs.	2010	aliter: a [Bioconductor] package f
20418340	r	FABIA: factor analysis for bicluster acquisition.	2010	ble as an [R package] on biocon
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20413636	java	PepC: proteomics software for identifying differentially expressed proteins based on spectral counting.	2010	mented in [java]. it has b
20413635	python	HangOut: generating clean PSI-BLAST profiles for domains with long insertions.	2010	mented in [python] 2.3 and r
20412558	r	BioPhysConnectoR: Connecting sequence information and biophysical models.	2010	with the [R package] biophysco
20410052	python	Inference of combinatorial Boolean rules of synergistic gene sets from cancer microarray datasets.	2010	ritten in [python] and r are
20410052	r	Inference of combinatorial Boolean rules of synergistic gene sets from cancer microarray datasets.	2010	in python [and R] are avail
20410051	c++	Supersplat--spliced RNA-seq alignment.	2010	mented in [C++], superspl
20400454	c++	HIV classification using the coalescent theory.	2010	mented in [C++] and the s
20398407	r	Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data.	2010	arr is an [R package] that cove
20395285	r	Picante: R tools for integrating phylogenies and ecology.	2010	vironment [written in R] and c, re
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20385730	perl	Quality assessment of protein model-structures using evolutionary conservation.	2010	a [perl] implement
20385013	java	web cellHTS2: a web-application for the analysis of high-throughput screening data.	2010	upporting [java] 1.5.0 can
20378558	r	BoolNet--an R package for generation, reconstruction and analysis of Boolean networks.	2010	olnet--an [R package] for gener
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20378555	java	Correction of sequencing errors in a mixed set of reads.	2010	the [java] source co
20375112	mathlab	Multilevel support vector regression analysis to identify condition-specific regulatory networks.	2010	he ml-svr [matlab] package c
20375111	r	partDSA: deletion/substitution/addition algorithm for partitioning the covariate space in prediction.	2010	dsa as an [R package].
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20370922	java	A highly efficient multi-core algorithm for clustering extremely large datasets.	2010	ed of our [java] based alg
20363732	java	Streamlining the construction of large-scale dynamic models using generic kinetic equations.	2010	e code in [java], is avail
20363730	java	ACCUSA--accurate SNP calling on draft genomes.	2010	rammed in [java] 6 and run
20363728	r	Supervised normalization of microarrays.	2010	an [R package] called sn
20346105	java	Moara: a Java library for extracting and normalizing gene and protein mentions.	2010	moara: a [java] library f
20338898	r	EBImage--an R package for image processing with applications to cellular phenotypes.	2010	image--an [R package] for image
20307295	java	In silico fragmentation for computer assisted identification of metabolite mass spectra.	2010	es and as [java] library.
20299327	java	ArchSchema: a tool for interactive graphing of related Pfam domain architectures.	2010	hema is a [java] web start
20299326	java	HALO--a Java framework for precise transcript half-life determination.	2010	halo--a [java] framework
20298548	mathlab	Gene regulatory networks modelling using a dynamic evolutionary hybrid.	2010	nted in a [matlab] toolbox a
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20223837	mathlab	Inferring cluster-based networks from differently stimulated multiple time-course gene expression data.	2010	a [matlab] implement
20223834	r	Integrative mixture of experts to combine clinical factors and gene markers.	2010	ed in the [R package] integrati
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20214778	java	Mayday--integrative analytics for expression data.	2010	ways. as [java] program,
20214776	mathlab	SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale.	2010	y coupled [matlab] scripts t
20208069	c++	Genome-wide synteny through highly sensitive sequence alignment: Satsuma.	2010	mented in [C++] on linux.
20207696	perl	Filtering error from SOLiD Output.	2010	ritten in [perl] and runs
20122197	c++	A hub-attachment based method to detect functional modules from confidence-scored protein interactions and expression profiles.	2010	a [C++] implement
20193060	perl	The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays.	2010	ackage of [perl] modules f
20189937	mathlab	Exploiting sequence similarity to validate the sensitivity of SNP arrays in detecting fine-scaled copy number variations.	2010	the [matlab] implement
20185407	c++	ESBTL: efficient PDB parser and data structure for the structural and geometric analysis of biological macromolecules.	2010	ghtweight [C++] library t
20181285	java	SpectraClassifier 1.0: a user friendly, automated MRS-based classifier-development system.	2010	(sc) is a [java] solution
20179076	r	GOSemSim: an R package for measuring semantic similarity among GO terms and gene products.	2010	emsim: an [R package] for measu
20179074	python	Domain adaptation for semantic role labeling in the biomedical domain.	2010	mented in [python] and c and
20176580	c++	An optimal experimental design approach to model discrimination in dynamic biochemical systems.	2010	mented in [C++] in the pa
20172942	r	CandiSNPer: a web tool for the identification of candidate SNPs for causal variants.	2010	d in perl [and R] and runs
20172942	perl	CandiSNPer: a web tool for the identification of candidate SNPs for causal variants.	2010	mented in [perl] and r and
20170493	r	A statistical framework for differential network analysis from microarray data.	2010	tions. an [R package] of our te
20163737	r	Potentials 'R' Us web-server for protein energy estimations with coarse-grained knowledge-based potentials.	2010	otentials ['R'] us web-se
20156990	r	Phybase: an R package for species tree analysis.	2010	ybase: an [R package] for speci
20147305	mathlab	Estimating replicate time shifts using Gaussian process regression.	2010	[matlab] code for
20147302	perl	Fast and SNP-tolerant detection of complex variants and splicing in short reads.	2010	ograms in [perl] are freel
20144191	r	Testing the additional predictive value of high-dimensional molecular data.	2010	ed in the [R package] globalbo
20130031	perl	Six Rossmannoid folds, including the Class I aminoacyl-tRNA synthetases, share a partial core with the anti-codon-binding domain of a Class II aminoacyl-tRNA synthetase.	2010	ritten in [perl] and c and
20130030	python	Identifying biologically relevant differences between metagenomic communities.	2010	[python] source co
20128918	r	BABAR: an R package to simplify the normalisation of common reference design microarray-based transcriptomic datasets.	2010	babar: an [R package] to simpli
20122279	c++	Multiple structure alignment and consensus identification for proteins.	2010	mented in [C++] and can b
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20110278	c++	BEDTools: a flexible suite of utilities for comparing genomic features.	2010	ritten in [C++]. source c
20110277	r	A hidden Ising model for ChIP-chip data analysis.	2010	ttp://www.[Bioconductor].org/.
20106819	c++	invertFREGENE: software for simulating inversions in population genetic data.	2010	[C++] source co
20106815	perl	iMotifs: an integrated sequence motif visualization and analysis environment.	2010	s for the [perl], ruby, r
20105306	python	Biana: a software framework for compiling biological interactions and analyzing networks.	2010	iana is a [python] framework
20097915	mathlab	WellReader: a MATLAB program for the analysis of fluorescence and luminescence reporter gene data.	2010	reader: a [matlab] program f
20096121	r	NeatMap--non-clustering heat map alternatives in R.	2010	map is an [R package] designed
20089513	r	rMAT--an R/Bioconductor package for analyzing ChIP-chip experiments.	2010	en source [R package], rmat, th
20081222	java	Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS.	2010	dely used [java] software
20080510	java	NEMO: a tool for analyzing gene and chromosome territory distributions from 3D-FISH experiments.	2010	and-alone [java] applicati
20080509	r	pegas: an R package for population genetics with an integrated-modular approach.	2010	pegas: an [R package] for popul
20080508	c++	MSMSpdbb: providing protein databases of closely related organisms to improve proteomic characterization of prokaryotic microbes.	2010	eloped in [C++] using the
20078892	java	OLS dialog: an open-source front end to the ontology lookup service.	2010	created a [java] front end
20074382	mathlab	LucidDraw: efficiently visualizing complex biochemical networks within MATLAB.	2010	ks within [matlab].
20071372	java	BamView: viewing mapped read alignment data in the context of the reference sequence.	2010	teractive [java] applicati
20070885	python	ETE: a python Environment for Tree Exploration.	2010	ete: a [python] environme
20061306	python	PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta.	2010	contains [python] bindings
20056731	r	CaliBayes and BASIS: integrated tools for the calibration, simulation and storage of biological simulation models.	2010	r with an [R package] for consu
20053276	python	PyMix--the python mixture package--a tool for clustering of heterogeneous biological data.	2010	ymix--the [python] mixture p
20040588	r	GWAF: an R package for genome-wide association analyses with family data.	2010	gwaf: an [R package] for genom
20040587	r	Mixtures of regression models for time course gene expression data: evaluation of initialization and random effects.	2010	able from [CRAN] (http://c
20031972	r	DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data.	2010	ment. the [R package] is availa
20028515	java	A response to information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments.	2009	available [java] implement
20028515	r	A response to information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments.	2009	in matlab [and R] by liu et
20028515	mathlab	A response to information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments.	2009	al. using [matlab]. also, ba
20021670	python	Using mechanistic Bayesian networks to identify downstream targets of the sonic hedgehog pathway.	2009	kage, the [python] environme
20015393	c	TargetSearch--a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data.	2009	functions [written in C] for speed
20015393	r	TargetSearch--a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data.	2009	search--a [Bioconductor] package f
20007740	c++	Tmod: toolbox of motif discovery.	2010	eloped in [C++] with the
20007253	r	PCIT: an R package for weighted gene co-expression networks based on partial correlation and information theory approaches.	2010	pcit: an [R package] for weigh
20003544	java	CHESS (CgHExpreSS): a comprehensive analysis tool for the analysis of genomic alterations and their effects on the expression profile of the genome.	2009	d in both [java] applicati
20003429	java	Graphle: Interactive exploration of large, dense graphs.	2009	teractive [java] applet. t
20003386	mathlab	Survival prediction from clinico-genomic models--a comparative study.	2009	ion data. [matlab] code for
20003283	r	An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation).	2009	en-source [R package] betr is a
19996165	mathlab	Temporal clustering by affinity propagation reveals transcriptional modules in Arabidopsis thaliana.	2010	[matlab] code for
19996163	c++	HIGEDA: a hierarchical gene-set genetics based algorithm for finding subtle motifs in biological sequences.	2010	mented in [C++] and suppo
19965880	mathlab	DataPflex: a MATLAB-based tool for the manipulation and visualization of multidimensional datasets.	2010	ported to [matlab] or .xls.
19958528	java	Bioclipse 2: a scriptable integration platform for the life sciences.	2009	mented in [java] and suppo
19942587	java	Extraction and comparison of gene expression patterns from 2D RNA in situ hybridization images.	2010	a [java] webstart
19942584	java	CMap3D: a 3D visualization tool for comparative genetic maps.	2010	ssing and [java]. binaries
19939831	java	Expertomica Cells: analysis of cell monolayer development.	2010	mented in [java] 6 and sup
19933825	java	EGAN: exploratory gene association networks.	2010	gan) is a [java] desktop a
19933824	r	A personalized microRNA microarray normalization method using a logistic regression model.	2010	asets and [R package] are avail
19933823	java	MIRAGAA--a methodology for finding coordinated effects of microRNA expression changes and genome aberrations in cancer.	2010	in r and [java], is avail
19933593	r	Joint estimation of DNA copy number from multiple platforms.	2010	the [R package] for mpcbs
19933163	mathlab	Bayesian variable selection for disease classification using gene expression data.	2010	a free [matlab] code to p
19933161	python	Annotation and merging of SBML models with semanticSBML.	2010	ritten in [python] and relea
19933158	r	Pathway analysis using random forests with bivariate node-split for survival outcomes.	2010	[R package] pwayrfsur
19930695	r	Regularized estimation of large-scale gene association networks using graphical Gaussian models.	2009	ed in the [R package] parcor ,
19914921	python	PyNAST: a flexible tool for aligning sequences to a template alignment.	2010	possible. [python] nearest a
19910308	r	edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.	2010	edger: a [Bioconductor] package f
19880372	java	Model aggregation: a building-block approach to creating large macromolecular regulatory networks.	2009	[java] implement
19880369	c++	MicroRazerS: rapid alignment of small RNA reads.	2010	the seqan [C++] library a
19880368	r	MATICCE: mapping transitions in continuous character evolution.	2010	ge in the [R language] for mappi
19874609	python	multiplierz: an extensible API based desktop environment for proteomics data analysis.	2009	igh-level [python] scripts,
19861356	c	Estimating population haplotype frequencies from pooled SNP data using incomplete database information.	2009	rce codes [written in C] (using gn
19861354	mathlab	Computational protein profile similarity screening for quantitative mass spectrometry experiments.	2010	a [matlab] toolbox i
19860866	mathlab	Gene ARMADA: an integrated multi-analysis platform for microarray data implemented in MATLAB.	2009	mented in [matlab].
19855105	r	DEGseq: an R package for identifying differentially expressed genes from RNA-seq data.	2010	egseq: an [R package] for ident
19828085	mathlab	A scale space approach for unsupervised feature selection in mass spectra classification for ovarian cancer detection.	2009	code, as [matlab] scripts,
19828078	perl	The Human EST Ontology Explorer: a tissue-oriented visualization system for ontologies distribution in human EST collections.	2009	relies on [perl] scripts a
19828075	perl	Extraction, integration and analysis of alternative splicing and protein structure distributed information.	2009	system of [perl] scripts h
19828071	perl	A Perl procedure for protein identification by Peptide Mass Fingerprinting.	2009	a [perl] procedure
19850754	r	The gputools package enables GPU computing in R.	2010	gputools [R package] is availa
19849862	perl	Direct calibration of PICKY-designed microarrays.	2009	files and [perl] programs
19832995	mathlab	Classification and biomarker identification using gene network modules and support vector machines.	2009	rrays.the [matlab] version o
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19811691	python	Exploratory visual analysis of conserved domains on multiple sequence alignments.	2009	ritten in [python] and using
19811679	r	NATbox: a network analysis toolbox in R.	2009	ox in the [language r] that hous
19814779	r	Deterministic Effects Propagation Networks for reconstructing protein signaling networks from multiple interventions.	2009	on of the [R package] nem ava
19811632	mathlab	Generation of Gene Ontology benchmark datasets with various types of positive signal.	2009	coded in [matlab] and is fr
19808880	r	HTqPCR: high-throughput analysis and visualization of quantitative real-time PCR data in R.	2009	d through [Bioconductor] or at htt
19808877	r	Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.	2009	n in perl [and R], for simu
19808877	perl	Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.	2009	ritten in [perl] and r, fo
19808875	java	Qupe--a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments.	2009	mented in [java] utilizing
19776214	java	SimCT: a generic tool to visualize ontology-based relationships for biological objects.	2009	specific [java] applet de
19773336	mathlab	Bayesian detection of non-sinusoidal periodic patterns in circadian expression data.	2009	[matlab] software
19773334	python	MOODS: fast search for position weight matrix matches in DNA sequences.	2009	operl and [biopython] toolkits.
19773334	c++	MOODS: fast search for position weight matrix matches in DNA sequences.	2009	ritten in [C++], with bin
19773334	perl	MOODS: fast search for position weight matrix matches in DNA sequences.	2009	e popular [bioperl] and biopy
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19747395	javascript	ICRPfinder: a fast pattern design algorithm for coding sequences and its application in finding potential restriction enzyme recognition sites.	2009	ser-based [javascript] applicati
19744993	javascript	QuickGO: a web-based tool for Gene Ontology searching.	2009	mented in [javascript], ajax and
19734153	c	Bi-correlation clustering algorithm for determining a set of co-regulated genes.	2009	developed [using C] and visua
19734151	java	Saint: a lightweight integration environment for model annotation.	2009	rted. the [java] source co
19720676	java	Identification of genes involved in the same pathways using a Hidden Markov Model-based approach.	2009	[java] source co
19713416	c++	A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis.	2009	[C++] source co
19713415	mathlab	ERNEST: a toolbox for chemical reaction network theory.	2009	lbox is a [matlab] package w
19712446	java	QPCR: Application for real-time PCR data management and analysis.	2009	web-based [java] applicati
19706745	r	integrOmics: an R package to unravel relationships between two omics datasets.	2009	omics: an [R package] to unrave
19706743	r	digeR: a graphical user interface R package for analyzing 2D-DIGE data.	2009	interface [R package] for analy
19706742	mathlab	Learning gene regulatory networks from gene expression measurements using non-parametric molecular kinetics.	2009	a [matlab] implement
19706180	java	Genoviz Software Development Kit: Java tool kit for building genomics visualization applications.	2009	ment kit: [java] tool kit
19698124	c++	MULTI-K: accurate classification of microarray subtypes using ensemble k-means clustering.	2009	well. the [C++] code and
19698094	python	p3d--Python module for structural bioinformatics.	2009	this the [python] scripting
19696046	java	PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains.	2009	requires [java], is avail
19696044	c++	Metabolite and reaction inference based on enzyme specificities.	2009	atlab and [C++] code is f
19696044	mathlab	Metabolite and reaction inference based on enzyme specificities.	2009	[matlab] and c++ c
19689961	java	CoCoa: a software tool for estimating the coefficient of coancestry from multilocus genotype data.	2009	ritten in [java].
19689961	c++	CoCoa: a software tool for estimating the coefficient of coancestry from multilocus genotype data.	2009	ritten in [C++], while th
19689956	python	CEAS: cis-regulatory element annotation system.	2009	the ceas [python] package i
19687029	java	SnoopCGH: software for visualizing comparative genomic hybridization data.	2009	ritten in [java] and is av
19679825	r	Stability and aggregation of ranked gene lists.	2009	available [Bioconductor] package g
19671693	r	Testing the hypothesis of tissue selectivity: the intersection-union test and a Bayesian approach.	2009	th matlab [and R] code that
19671693	mathlab	Testing the hypothesis of tissue selectivity: the intersection-union test and a Bayesian approach.	2009	both [matlab] and r cod
19671691	java	T-REKS: identification of Tandem REpeats in sequences with a K-meanS based algorithm.	2009	mented in [java], the prog
19661241	r	R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips.	2009	the crlmm [Bioconductor] package i
19656385	java	Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels.	2009	ritten in [java], and can
19654119	r	ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data.	2009	rtread: a [Bioconductor] package f
19654115	r	Multiple testing in genome-wide association studies via hidden Markov models.	2009	an [R package] plis has
19654113	java	The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets.	2009	mented in [java] that supp
19653903	mathlab	Generating rate equations for complex enzyme systems by a computer-assisted systematic method.	2009	athml and [matlab] output fi
19648135	r	Gene ranking and biomarker discovery under correlation.	2009	ed in the [R package] 'st', whi
19646231	java	sscMap: an extensible Java application for connecting small-molecule drugs using gene-expression signatures.	2009	xtensible [java] applicati
19640299	r	CLEAN: CLustering Enrichment ANalysis.	2009	an add-on [R package] and can b
19628503	mathlab	Modified variational Bayes EM estimation of hidden Markov tree model of cell lineages.	2009	the [matlab] code for
19628502	r	Moderated effect size and P-value combinations for microarray meta-analyses.	2009	an [R package] metama is
19620098	perl	Benchmarking homology detection procedures with low complexity filters.	2009	[perl] scripts f
19607672	perl	OrthoSelect: a protocol for selecting orthologous groups in phylogenomics.	2009	ritten in [perl] and runs
19605418	c++	DiProGB: the dinucleotide properties genome browser.	2009	mented in [C++] and suppo
19602528	mathlab	Expertomica metabolite profiling: getting more information from LC-MS using the stochastic systems approach.	2009	[matlab] scripts w
19589155	r	puma: a Bioconductor package for propagating uncertainty in microarray analysis.	2009	puma: a [Bioconductor] package f
19578173	python	FRED--a framework for T-cell epitope detection.	2009	mented in [python] in a modu
19578040	c++	TreeTime: an extensible C++ software package for Bayesian phylogeny reconstruction with time-calibration.	2009	xtensible [C++] software
19570806	c++	k-link EST clustering: evaluating error introduced by chimeric sequences under different degrees of linkage.	2009	ritten in [C++].
19561337	java	HAPLOWSER: a whole-genome haplotype browser for personal genome and metagenome.	2009	ritten in [java], supports
19561019	r	A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry.	2009	resent an [R package] ('massarr
19558728	mathlab	DOTcvpSB, a software toolbox for dynamic optimization in systems biology.	2009	ritten in [matlab] and provi
19534756	perl	The Mycoplasma conjunctivae genome sequencing, annotation and analysis.	2009	ected via [perl] scripts.
19534753	java	RetroTector online, a rational tool for analysis of retroviral elements in small and medium size vertebrate genomic sequences.	2009	dependent [java] program f
19534749	java	A bioinformatics knowledge discovery in text application for grid computing.	2009	ritten in [java] on globus
19534746	java	Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application.	2009	separate [java] applicati
19534737	mathlab	'Brukin2D': a 2D visualization and comparison tool for LC-MS data.	2009	built in [matlab] 7.4, whic
19542152	java	SHREC: a short-read error correction method.	2009	en-source [java] implement
19538731	r	designGG: an R-package and web tool for the optimal design of genetical genomics experiments.	2009	igngg, an [R package] for desig
19528086	r	PROMISE: a tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables.	2009	able as a [Bioconductor] package f
19528083	java	De novo transcriptome assembly with ABySS.	2009	mented in [java] using the
19528083	c++	De novo transcriptome assembly with ABySS.	2009	mented in [C++]. the para
19505947	c++	Rapid detection, classification and accurate alignment of up to a million or more related protein sequences.	2009	a [C++] implement
19505945	c++	trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.	2009	ritten in [C++], it is po
19505944	mathlab	Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood.	2009	lable for [matlab] and the p
19505942	r	Importing ArrayExpress datasets into R/Bioconductor.	2009	from the [Bioconductor] project a
19505940	java	Identifying the topology of protein complexes from affinity purification assays.	2009	a [java] implement
19497936	perl	ABACAS: algorithm-based automatic contiguation of assembled sequences.	2009	mented in [perl] and is fr
19497932	perl	Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA.	2009	mented in [perl] and relie
19486540	c	Fpocket: an open source platform for ligand pocket detection.	2009	en in the [C programming] language,
19478022	perl	Genotype-phenotype associations: substitution models to detect evolutionary associations between phenotypic variables and genotypic evolutionary rate.	2009	[perl] and hyphy
19478016	java	Identifying novel constrained elements by exploiting biased substitution patterns.	2009	nted in a [java] software
19478010	java	Efficient exact motif discovery.	2009	mented in [java]. it can b
19477986	c++	Multi-locus match probability in a finite population: a fundamental difference between the Moran and Wright-Fisher models.	2009	a [C++] implement
19477983	mathlab	Fewer permutations, more accurate P-values.	2009	the [matlab] code can
19468055	r	NTAP: for NimbleGen tiling array ChIP-chip data analysis.	2009	d in perl [and R] and can b
19468055	perl	NTAP: for NimbleGen tiling array ChIP-chip data analysis.	2009	mented in [perl] and r and
19468054	r	rtracklayer: an R package for interfacing with genome browsers.	2009	layer: an [R package] for inter
19468053	java	Using chemical organization theory for model checking.	2009	ata and a [java] applet to
19463149	r	Differential splicing using whole-transcript microarrays.	2009	ble as an [R package].
19460889	python	An active registry for bioinformatics web services.	2009	with php, [python], mysql an
19447787	r	Gradient lasso for Cox proportional hazards model.	2009	[R package] glcoxph i
19442304	r	flowClust: a Bioconductor package for automated gating of flow cytometry data.	2009	eloped an [R package] called fl
19439563	java	Apollo: a community resource for genome annotation editing.	2009	ollo is a [java] applicati
19435744	perl	Generating linkage mapping files from Affymetrix SNP chip data.	2009	agen is a [perl] tool that
19435742	mathlab	Robust synthetic biology design: stochastic game theory approach.	2009	oolbox in [matlab]. finally,
19420051	r	RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions.	2009	ble as an [R package] from cran
19414529	r	apLCMS--adaptive processing of high-resolution LC/MS data.	2009	ted in an [R package] aplcms, w
19401401	java	baobabLUNA: the solution space of sorting by reversals.	2009	mented in [java] is freely
19401399	python	Affinity Density: a novel genomic approach to the identification of transcription factor regulatory targets.	2009	mented in [python], lisp, r
19398451	r	penalizedSVM: a R-package for feature selection SVM classification.	2009	d. in the [R package] 'penalize
19398447	r	GeneRegionScan: a Bioconductor package for probe-level analysis of specific, small regions of the genome.	2009	dependent [R package] available
19389734	c++	MetaTISA: Metagenomic Translation Initiation Site Annotator for improving gene start prediction.	2009	the [C++] source co
19389732	python	KIRMES: kernel-based identification of regulatory modules in euchromatic sequences.	2009	the [python] source co
19376826	java	A stochastic model for the evolution of metabolic networks with neighbor dependence.	2009	ampler in [java] is availa
19376823	c++	A local multiple alignment method for detection of non-coding RNA sequences.	2009	the [C++] source co
19374774	r	Data-driven normalization strategies for high-throughput quantitative RT-PCR.	2009	are as an [R package] qpcrnorm
19369502	java	Fluctuation analysis CalculatOR: a web tool for the determination of mutation rate using Luria-Delbruck fluctuation analysis.	2009	tten as a [java] applet, r
19358741	r	flowCore: a Bioconductor package for high throughput flow cytometry.	2009	ls in the [R package] flowcore
19351618	mathlab	Enrichment constrained time-dependent clustering analysis for finding meaningful temporal transcription modules.	2009	data and [matlab] code are
19349284	r	Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x.	2009	n source. [Bioconductor] 2.3 packa
19307241	r	BioconductorBuntu: a Linux distribution that implements a web-based DNA microarray analysis server.	2009	ed by the [Bioconductor] project,
19307239	r	KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor.	2009	in r and [Bioconductor].
19304878	python	Biopython: freely available Python tools for computational molecular biology and bioinformatics.	2009	available [python] tools for
19297349	java	DASher: a stand-alone protein sequence client for DAS, the Distributed Annotation System.	2009	en-source [java] das clien
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19289448	mathlab	Gaussian process regression bootstrapping: exploring the effects of uncertainty in time course data.	2009	[matlab] code for
19289444	python	GS2: an efficiently computable measure of GO-based similarity of gene sets.	2009	en-source [python] library.
19289443	java	A method and program for estimating graphical models for linkage disequilibrium that scale linearly with the number of loci, and their application to gene drop simulation.	2009	[java] classes a
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19286833	c++	Statistical detection of cooperative transcription factors with similarity adjustment.	2009	s well as [C++] source co
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19276151	r	The tspair package for finding top scoring pair classifiers in R.	2009	cribe the [R package], tspair,
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19269988	c++	RNATOPS-W: a web server for RNA structure searches of genomes.	2009	mand line [C++] software
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19244389	r	Boosting for high-dimensional time-to-event data with competing risks.	2009	ed in the [R package] coxboost
19244386	mathlab	BISEN: Biochemical Simulation Environment.	2009	ms in the [matlab] computing
19244385	java	PLATINUM: a web tool for analysis of hydrophobic/hydrophilic organization of biomolecular complexes.	2009	requires [java] 5 or high
19237448	r	PAnnBuilder: an R package for assembling proteomic annotation data.	2009	ilder: an [R package] for assem
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19225024	r	gcExplorer: interactive exploration of gene clusters.	2009	t the new [R package] gcexplore
19223449	javascript	OnTheFly: a tool for automated document-based text annotation, data linking and network generation.	2009	s to them [javascript] code to i
19218352	javascript	CGAS: comparative genomic analysis server.	2009	nchronous [javascript] and xml (
19213739	c++	Enumeration of condition-dependent dense modules in protein interaction networks.	2009	a [C++] implement
19211573	c	STEM: species tree estimation using maximum likelihood for gene trees under coalescence.	2009	en in the [C language] to obtain
19200358	r	EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data.	2009	on r and [Bioconductor] packages
19193733	java	Radié: visualizing taxon properties and parsimonious mappings using a radial phylogenetic tree.	2009	active 3d [java] applicati
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19188192	c++	Accurate identification of orthologous segments among multiple genomes.	2009	nted as a [C++] program.
19181685	java	NOBLAST and JAMBLAST: New Options for BLAST and a Java Application Manager for BLAST results.	2009	ast and a [java] applicati
19181683	r	CORNA: testing gene lists for regulation by microRNAs.	2009	ble as an [R package] from http
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19176559	mathlab	A novel comprehensive wave-form MS data processing method.	2009	xample of [matlab] scripts u
19176556	r	Parallelized prediction error estimation for evaluation of high-dimensional models.	2009	ed by the [R package] peperr, w
19176555	r	A flexible rank-based framework for detecting copy number aberrations from array data.	2009	an [R package] rankcopy
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19176547	c++	A novel meta-analysis method exploiting consistency of high-throughput experiments.	2009	a [C++] implement
19171029	r	Evaluating the impact of scoring parameters on the structure of intra-specific genetic variation using RawGeno, an R package for automating AFLP scoring.	2009	wgeno, an [R package] for autom
19168913	java	AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context.	2009	the [java] code for
19166610	javascript	Genome Projector: zoomable genome map with multiple views.	2009	nchronous [javascript] and xml (
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19134227	r	PreP+07: improvements of a user friendly tool to preprocess and analyse microarray data.	2009	ctions in [Bioconductor] using a t
19114008	r	WGCNA: an R package for weighted correlation network analysis.	2008	wgcna: an [R package] for weigh
19114001	r	SPRINT: a new parallel framework for R.	2008	systems, [using R], but with
19112081	mathlab	Differential dependency network analysis to identify condition-specific topological changes in biological networks.	2009	the ddn [matlab] toolbox a
19109877	r	SimHap GUI: an intuitive graphical user interface for genetic association analysis.	2008	he simhap [R package], while pr
19106121	r	arrayQualityMetrics--a bioconductor package for quality assessment of microarray data.	2009	etrics--a [Bioconductor] package f
19106120	python	AnnotationSketch: a genome annotation drawing library.	2009	ges ruby, [python] and lua.
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19095699	mathlab	Probabilistic assignment of formulas to mass peaks in metabolomics experiments.	2009	document, [matlab] code, dat
19087293	perl	A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data.	2008	cripts in [perl], bioperl,
19087285	java	SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes.	2008	e through [java] webstart
19074958	r	rHVDM: an R package to predict the activity and targets of a transcription factor.	2009	rhvdm: an [R package] to predic
19073589	r	SIMoNe: Statistical Inference for MOdular NEtworks.	2009	the [R package] simone (s
19073588	mathlab	Matrix correlations for high-dimensional data: the modified RV-coefficient.	2009	the [matlab] m-files o
19068132	java	The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results.	2008	en source [java] applicati
19043077	r	Programs for calculating the statistical powers of detecting susceptibility genes in case-control studies based on multistage designs.	2009	udy using [R language]. in our p
19040729	r	Highly sensitive feature detection for high resolution LC/MS.	2008	into the [Bioconductor] r-package
19019849	c++	A multivariate test of association.	2009	a [C++] implement
19015130	c++	Prediction of translation initiation site for microbial genomes with TriTISA.	2009	the [C++] source co
19014642	r	CrossHybDetector: detection of cross-hybridization events in DNA microarray experiments.	2008	ithin the [CRAN] project.
19014540	r	A Web-based and Grid-enabled dChip version for the analysis of large sets of gene expression data.	2008	e r-based [Bioconductor] and dchip
19014535	perl	Extension of the COG and arCOG databases by amino acid and nucleotide sequences.	2008	s such as [perl] applied t
19014471	r	Standardized high-throughput evaluation of cell-based compound screens.	2008	s a novel [R package] with a tc
18990722	r	A novel signaling pathway impact analysis.	2009	ted as an [R package] available
18990721	java	DNAPlotter: circular and linear interactive genome visualization.	2009	teractive [java] applicati
18984599	java	TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops.	2009	ed from a [java] graphical
18980677	r	Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information.	2008	from the [R package] archive c
18977780	python	PConPy--a Python module for generating 2D protein maps.	2008	pconpy--a [python] module fo
18977779	r	Model-based analysis of non-specific binding for background correction of high-density oligonucleotide microarrays.	2009	ed in the [R language] and can b
18974169	mathlab	Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models.	2008	[matlab] code is a
18974073	mathlab	Identifying molecular markers associated with classification of genotypes by External Logistic Biplots.	2008	the [matlab] code for
18959772	r	minet: A R/Bioconductor package for inferring large transcriptional networks using mutual information.	2008	from the [Bioconductor] website.
18957118	java	MetaMine--a tool to detect and analyse gene patterns in their environmental context.	2008	mented in [java] and provi
18953044	r	BASH: a tool for managing BeadArray spatial artefacts.	2008	beadarray [Bioconductor] package (
18953044	bash	BASH: a tool for managing BeadArray spatial artefacts.	2008	e present [bash], a tool f
18945685	python	CARPET: a web-based package for the analysis of ChIP-chip and expression tiling data.	2008	of perl, [python] and r scr
18945685	r	CARPET: a web-based package for the analysis of ChIP-chip and expression tiling data.	2008	l, python [and R] scripts,
18945685	perl	CARPET: a web-based package for the analysis of ChIP-chip and expression tiling data.	2008	a set of [perl], python a
18940826	java	QGene 4.0, an extensible Java QTL-analysis platform.	2008	xtensible [java] qtl-analy
18937846	mathlab	Assessment of protein set coherence using functional annotations.	2008	networks. [matlab] code and
18925941	r	CMA: a comprehensive Bioconductor package for supervised classification with high dimensional data.	2008	rehensive [Bioconductor] package f
18922808	r	Reconstructing tumor-wise protein expression in tissue microarray studies using a Bayesian cell mixture model.	2008	[R package] to fit cm
18851737	r	Probabilistic base calling of Solexa sequencing data.	2008	f 15%. an [R package] is provid
18842601	c	A flexible forward simulator for populations subject to selection and demography.	2008	en in the [C programming] language)
18842599	r	GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus.	2008	dition, a [Bioconductor] package,
18842599	mathlab	GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus.	2008	esponding [matlab] implement
18842147	mathlab	Detection of the dominant direction of information flow and feedback links in densely interconnected regulatory networks.	2008	f f90 and [matlab] implement
18819939	r	Identifying differentially expressed subnetworks with MMG.	2008	htm, from [CRAN], and has
18818216	fortran	Bayesian learning of biological pathways on genomic data assimilation.	2008	the [fortran] source co
18817533	java	Presenting and exploring biological pathways with PathVisio.	2008	etely new [java] implement
18812364	java	Integrating and annotating the interactome using the MiMI plugin for cytoscape.	2009	hed using [java] webstart
18805798	java	MS-BID: a Java package for label-free LC-MS-based comparative proteomic analysis.	2008	ms-bid: a [java] package f
18803830	java	GlycomeDB - integration of open-access carbohydrate structure databases.	2008	arge. the [java] applicati
18793458	java	Clustering ionic flow blockade toggles with a mixture of HMMs.	2008	arning. a [java] implement
18796477	python	tCal: transcriptional probability calculator using thermodynamic model.	2008	odel in a [python] module, '
18790795	r	Gene set enrichment analysis using linear models and diagnostics.	2008	ilable as [Bioconductor] package g
18789148	mathlab	Increasing the efficiency of bacterial transcription simulations: when to exclude the genome without loss of accuracy.	2008	a simple [matlab] user inte
18784119	java	F-Seq: a feature density estimator for high-throughput sequence tags.	2008	en in the [java] language
18784117	fortran	Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks.	2008	[fortran] 90 source
18776194	java	STREAM: Static Thermodynamic REgulAtory Model of transcription.	2008	requires [java] version 5
18757875	c++	PREDICT-2ND: a tool for generalized protein local structure prediction.	2008	required [C++] library i
18755046	java	FERN - a Java framework for stochastic simulation and evaluation of reaction networks.	2008	fern - a [java] framework
18753155	r	Supervised principal component analysis for gene set enrichment of microarray data with continuous or survival outcomes.	2008	hod in an [R package].
18753153	java	StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees.	2008	ge in the [java] programmi
18721485	perl	SynBlast: assisting the analysis of conserved synteny information.	2008	ritten in [perl] is availa
18718947	r	Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores.	2008	eemix: an [R package] for estim
18718946	r	Eigen-R2 for dissecting variation in high-dimensional studies.	2008	lable via [Bioconductor].
18718939	r	Analyzing gene perturbation screens with nested effects models in R and bioconductor.	2008	en in the [R language] and freel
18710873	r	Inference of structure in subdivided populations at low levels of genetic differentiation--the correlated allele frequencies model revisited.	2008	.0 of the [R package] geneland.
18691414	r	Methylation Linear Discriminant Analysis (MLDA) for identifying differentially methylated CpG islands.	2008	ilable at [CRAN] 1. this a
18689843	mathlab	Gaussian process modelling of latent chemical species: applications to inferring transcription factor activities.	2008	ilable in [matlab] from http
18689838	c++	Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry.	2008	[C++] code impl
18689828	mathlab	Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules.	2008	mented in [matlab] (mathwork
18689821	python	Optimal spliced alignments of short sequence reads.	2008	n c++ and [python] are avail
18689821	c++	Optimal spliced alignments of short sequence reads.	2008	mented in [C++] and pytho
18689819	java	Efficient representation and P-value computation for high-order Markov motifs.	2008	form of a [java] objectori
18689812	mathlab	Comparison of vocabularies, representations and ranking algorithms for gene prioritization by text mining.	2008	the [matlab] code of t
18689808	java	BioJava: an open-source framework for bioinformatics.	2008	nt in the [java] programmi
18687127	r	Performing statistical analyses on quantitative data in Taverna workflows: an example using R and maxdBrowse to identify differentially-expressed genes from microarray data.	2008	n example [using R] and maxdb
18687127	mathlab	Performing statistical analyses on quantitative data in Taverna workflows: an example using R and maxdBrowse to identify differentially-expressed genes from microarray data.	2008	as r and [matlab] require p
18682425	perl	BLogo: a tool for visualization of bias in biological sequences.	2008	logo. the [perl] source co
18676972	r	Predicting pathway membership via domain signatures.	2008	the [R package] gene2path
18676417	java	Large-scale computation of elementary flux modes with bit pattern trees.	2008	tation in [java], with int
18676417	mathlab	Large-scale computation of elementary flux modes with bit pattern trees.	2008	tion into [matlab] and suppo
18667443	r	A fast Bayesian change point analysis for the segmentation of microarray data.	2008	duced the [R package] bcp (baye
18662925	python	Mixture models for protein structure ensembles.	2008	the [python] source co
18641010	c	Message-passing algorithms for the prediction of protein domain interactions from protein-protein interaction data.	2008	a [C language] implement
18638416	r	Assessing probe-specific dye and slide biases in two-color microarray data.	2008	ance. the [R package] lmgene wh
18635570	r	mlegp: statistical analysis for computer models of biological systems using R.	2008	scribe an [R package], mlegp, t
18635567	r	A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all?	2008	ted in an [R package] called su
18635566	java	ProCope--protein complex prediction and evaluation.	2008	rocope, a [java] software
18628290	mathlab	Artificial neural network for prediction of antigenic activity for a major conformational epitope in the hepatitis C virus NS3 protein.	2008	[matlab] code is a
18621757	mathlab	Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli.	2008	all [matlab] files use
18620604	java	PRESTO: rapid calculation of order statistic distributions and multiple-testing adjusted P-values via permutation for one and two-stage genetic association studies.	2008	ble file, [java] source co
18614583	mathlab	Dynamical modeling and multi-experiment fitting with PottersWheel.	2008	gned as a [matlab] toolbox a
18613966	r	A unified approach to false discovery rate estimation.	2008	from the [R package] archive c
18606607	c++	ProteoWizard: open source software for rapid proteomics tools development.	2008	ng modern [C++] technique
18599518	java	FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology.	2008	running a [java] runtime e
18596077	r	ChemmineR: a compound mining framework for R.	2008	ed by the [R package] chemminer
18593718	java	BioMAJ: a flexible framework for databanks synchronization and processing.	2008	data. the [java] applicati
18593717	r	PuReD-MCL: a graph-based PubMed document clustering methodology.	2008	e in perl [and R] are avail
18593717	perl	PuReD-MCL: a graph-based PubMed document clustering methodology.	2008	e code in [perl] and r are
18586744	mathlab	MicroRNA prediction with a novel ranking algorithm based on random walks.	2008	rammed in [matlab] on window
18586742	c++	Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space.	2008	ervice. a [C++] implement
18586734	python	Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification.	2008	[python] and c sou
18586722	mathlab	Protein complex identification by supervised graph local clustering.	2008	[matlab] implement
18586716	python	Contact replacement for NMR resonance assignment.	2008	dependent [python] code. the
18586711	mathlab	Combinatorial influence of environmental parameters on transcription factor activity.	2008	the [matlab] code is a
18586707	mathlab	Alignment and classification of time series gene expression in clinical studies.	2008	[matlab] implement
18579568	java	PRIMEGENS-v2: genome-wide primer design for analyzing DNA methylation patterns of CpG islands.	2008	the c and [java] programmi
18541052	mathlab	Quantitative analysis of numerical solvers for oscillatory biomolecular system models.	2008	s. we use [matlab] numerical
18567917	c++	Database indexing for production MegaBLAST searches.	2008	the ncbi [C++] toolkit.
18544547	r	Microarray-based classification and clinical predictors: on combined classifiers and additional predictive value.	2008	available [R package] 'maclinic
18544546	perl	Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data.	2008	seed is a [perl] program t
18535082	mathlab	Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification.	2008	sifier in [matlab] is provid
18515276	r	Sparse kernel methods for high-dimensional survival data.	2008	nse as an [R package] and can b
18513431	mathlab	poolHiTS: a shifted transversal design based pooling strategy for high-throughput drug screening.	2008	hits. the [matlab] codes for
18511468	java	Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration.	2008	izer is a [java] applicati
18511467	c++	Efficient functional clustering of protein sequences using the Dirichlet process.	2008	mented as [C++] software
18507856	r	TileQC: a system for tile-based quality control of Solexa data.	2008	en in the [R language]. tileqc p
18501020	perl	Predikin and PredikinDB: a computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites.	2008	nd (ii) a [perl] module, w
18501020	javascript	Predikin and PredikinDB: a computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites.	2008	ritten in [javascript].
18499696	c++	The Sleipnir library for computational functional genomics.	2008	sleipnir [C++] library i
18499695	c	EM-random forest and new measures of variable importance for multi-locus quantitative trait linkage analysis.	2008	for emrf [written in C] is availa
18485197	javascript	Visualization of large influenza virus sequence datasets using adaptively aggregated trees with sampling-based subscale representation.	2008	mented in [javascript] within th
18482995	r	qpcR: an R package for sigmoidal model selection in quantitative real-time polymerase chain reaction analysis.	2008	qpcr: an [R package] for sigmo
18480100	java	Computing chemical organizations in biological networks.	2008	ata and a [java] implement
18477576	perl	A distance metric for a class of tree-sibling phylogenetic networks.	2008	the [perl] package b
18474508	c++	DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony.	2008	ritten in [C++].
18474506	java	Malin: maximum likelihood analysis of intron evolution in eukaryotes.	2008	and-alone [java] applicati
18474505	java	FunSiP: a modular and extensible classifier for the prediction of functional sites in DNA.	2008	and-alone [java] applicati
18474116	perl	Discovery and assembly of repeat family pseudomolecules from sparse genomic sequence data using the Assisted Automated Assembler of Repeat Families (AAARF) algorithm.	2008	ritten in [perl] and with
18467348	r	lumi: a pipeline for processing Illumina microarray.	2008	lumi is a [Bioconductor] package e
18467347	java	Microbial genotype-phenotype mapping by class association rule mining.	2008	de of the [java] implement
18467344	c++	PatMaN: rapid alignment of short sequences to large databases.	2008	the [C++] source co
18453554	c++	An efficient method to identify differentially expressed genes in microarray experiments.	2008	the [C++] code to i
18450812	r	A correction for estimating error when using the Local Pooled Error Statistical Test.	2008	ed in the [R language] and can b
18450810	c++	quantiNemo: an individual-based program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation.	2008	coded in [C++] using an
18447951	java	Implementing EM and Viterbi algorithms for Hidden Markov Model in linear memory.	2008	optimized [java] implement
18445606	java	jSquid: a Java applet for graphical on-line network exploration.	2008	jsquid: a [java] applet fo
18445289	java	An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions.	2008	teractive [java] applicati
18441000	r	fdrtool: a versatile R package for estimating local and tail area-based false discovery rates.	2008	versatile [R package] for estim
18440999	c++	MAMOT: hidden Markov modeling tool.	2008	mented in [C++], and is d
18430251	perl	VariVis: a visualisation toolkit for variation databases.	2008	executing [perl] cgi scrip
18424458	java	Fast grid layout algorithm for biological networks with sweep calculation.	2008	[java] implement
18416814	mathlab	anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data.	2008	eloped in [matlab] a general
18387211	perl	Version VI of the ESTree db: an improved tool for peach transcriptome analysis.	2008	a [perl] modular p
18413327	r	Analysing georeferenced population genetics data with Geneland: a new algorithm to deal with null alleles and a friendly graphical user interface.	2008	nse as an [R package] on the co
18407922	c	Divisive Correlation Clustering Algorithm (DCCA) for grouping of genes: detecting varying patterns in expression profiles.	2008	developed [using C] and visua
18405375	java	uShuffle: a useful tool for shuffling biological sequences while preserving the k-let counts.	2008	ode in c, [java], and c#,
18405375	python	uShuffle: a useful tool for shuffling biological sequences while preserving the k-let counts.	2008	perl and [python] are provi
18405375	perl	uShuffle: a useful tool for shuffling biological sequences while preserving the k-let counts.	2008	tions for [perl] and pytho
18400774	c++	A system for generating transcription regulatory networks with combinatorial control of transcription.	2008	enco is a [C++] command l
18397895	r	adegenet: a R package for the multivariate analysis of genetic markers.	2008	egenet: a [R package] for the m
18390879	java	UniProtJAPI: a remote API for accessing UniProt data.	2008	created a [java] library n
18375965	python	CompariMotif: quick and easy comparisons of sequence motifs.	2008	en source [python] modules u
18371228	java	A perl package and an alignment tool for phylogenetic networks.	2008	veloped a [java] applet th
18371228	perl	A perl package and an alignment tool for phylogenetic networks.	2008	a [perl] package a
18366796	java	Chromhome: a rich internet application for accessing comparative chromosome homology maps.	2008	nterprise [java] platform
18356193	mathlab	Bayesian inference of the sites of perturbations in metabolic pathways via Markov chain Monte Carlo.	2008	[matlab] code used
18353790	perl	A suite of Perl modules for handling microarray data.	2008	suite of [perl] modules f
18344518	r	Unequal group variances in microarray data analyses.	2008	[R package] to perfor
18344248	mathlab	Fitting a geometric graph to a protein-protein interaction network.	2008	[matlab] code impl
18325927	mathlab	Merging two gene-expression studies via cross-platform normalization.	2008	s and xpn [matlab] code are
18325106	r	Empirical Bayes analysis of single nucleotide polymorphisms.	2008	le in the [R package] siggenes
18318917	r	Normalization of oligonucleotide arrays based on the least-variant set of genes.	2008	ation. an [R package] called lv
18318908	java	Goldsurfer2 (Gs2): a comprehensive tool for the analysis and visualization of genome wide association studies.	2008	mented in [java] and can b
18312684	java	A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation.	2008	a [java] applicati
18296463	r	CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms.	2008	atistical [language r]. we encou
18292114	mathlab	MMG: a probabilistic tool to identify submodules of metabolic pathways.	2008	[matlab] code is a
18284666	r	K-OPLS package: kernel-based orthogonal projections to latent structures for prediction and interpretation in feature space.	2008	or matlab [and R], licensed
18284666	mathlab	K-OPLS package: kernel-based orthogonal projections to latent structures for prediction and interpretation in feature space.	2008	rithm for [matlab] and r, li
18267948	mathlab	Complexity reduction of biochemical rate expressions.	2008	box 2 for [matlab], which is
18263642	java	Interactive visualization software for exploring phylogenetic trees and clades.	2008	ste) is a [java] applicati
18252739	r	ITALICS: an algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays.	2008	the [R package] italics (
18252737	java	LibSBML: an API library for SBML.	2008	mon lisp, [java], python,
18252737	python	LibSBML: an API library for SBML.	2008	sp, java, [python], perl, ma
18252737	c++	LibSBML: an API library for SBML.	2008	iso c and [C++], provides
18252737	perl	LibSBML: an API library for SBML.	2008	, python, [perl], matlab a
18252737	mathlab	LibSBML: an API library for SBML.	2008	on, perl, [matlab] and octav
18251994	java	The VirusBanker database uses a Java program to allow flexible searching through Bunyaviridae sequences.	2008	se uses a [java] program t
18251993	java	A comparison of common programming languages used in bioinformatics.	2008	c++, c#, [java], perl and
18251993	python	A comparison of common programming languages used in bioinformatics.	2008	perl and [python].
18251993	c++	A comparison of common programming languages used in bioinformatics.	2008	ted in c, [C++], c#, java
18251993	perl	A comparison of common programming languages used in bioinformatics.	2008	c#, java, [perl] and pytho
18245128	r	Using flowViz to visualize flow cytometry data.	2008	ble as an [R package] from the
18245126	c++	Model-based Bayesian clustering (MBBC).	2008	ox, r and [C++], taking a
18245126	r	Model-based Bayesian clustering (MBBC).	2008	un the ox [and R] programs
18245124	perl	ONTO-PERL: an API for supporting the development and analysis of bio-ontologies.	2008	://search.[CPAN].org/dist/
18238804	java	Interoperability with Moby 1.0--it's better than sharing your toothbrush!	2008	perl and [java] code-base
18238804	perl	Interoperability with Moby 1.0--it's better than sharing your toothbrush!	2008	upporting [perl] and java
18237431	r	AWclust: point-and-click software for non-parametric population structure analysis.	2008	ted as an [R package]. the soft
18237374	r	SIGffRid: a tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically driven statistics.	2008	es finder [using R]'mes to se
18227118	java	Utility library for structural bioinformatics.	2008	ritten in [java] language
18227117	r	Estimating large-scale signaling networks through nested effect models with intervention effects from microarray data.	2008	ithin the [Bioconductor] r-package
18227116	java	TaxonGap: a visualization tool for intra- and inter-species variation among individual biomarkers.	2008	xecutable [java] archive f
18221524	perl	TOBFAC: the database of tobacco transcription factors.	2008	used the [perl] programmi
18221524	javascript	TOBFAC: the database of tobacco transcription factors.	2008	mented in [javascript] and perl
18218657	perl	Colorstock, SScolor, Ratón: RNA alignment visualization tools.	2008	scolor, a [perl] script th
18208605	r	SignS: a parallelized, open-source, freely available, web-based tool for gene selection and molecular signatures for survival and censored data.	2008	tool and [R package] for gene
18205906	perl	T2prhd: a tool to study the patterns of repeat evolution.	2008	nted in a [perl] script (t
18204060	r	HCGene: a software tool to support the hierarchical classification of genes.	2008	the [R package] hcgene (h
18204055	r	Estimation and assessment of raw copy numbers at the single locus level.	2008	en-source [R package] named aro
18204054	r	Using repeated measurements to validate hierarchical gene clusters.	2008	oped in c [and R] languages
18203773	r	Multiple testing on the directed acyclic graph of gene ontology.	2008	le on www.[Bioconductor].org.
18202028	perl	The SGN comparative map viewer.	2008	oriented [perl], with a s
18201381	r	Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'.	2008	compliant [R package] 'annotati
18194961	mathlab	Pinnacle: a fast, automatic and accurate method for detecting and quantifying protein spots in 2-dimensional gel electrophoresis data.	2008	[matlab] code to i
18194537	java	NestedMICA as an ab initio protein motif discovery tool.	2008	ritten in [java], is drive
18187444	java	Effect of spatial distribution of T-Cells and HIV load on HIV progression.	2008	c++ and [java] have been
18187444	c++	Effect of spatial distribution of T-Cells and HIV load on HIV progression.	2008	[C++] and java
18187443	mathlab	A feed-forward loop guarantees robust behavior in Escherichia coli carbohydrate uptake.	2008	[matlab] files for
18187441	r	OutlierD: an R package for outlier detection using quantile regression on mass spectrometry data.	2008	lierd: an [R package] for outli
18184687	mathlab	A hybrid model for robust detection of transcription factor binding sites.	2008	a [matlab] implement
18184432	c++	SeqAn an efficient, generic C++ library for sequence analysis.	2008	, generic [C++] library f
18180239	c++	FAST: Fourier transform based algorithms for significance testing of ungapped multiple alignments.	2008	includes [C++] implement
18177498	r	Extending pathways based on gene lists using InterPro domain signatures.	2008	lable via [Bioconductor].
18175769	mathlab	Structural systems identification of genetic regulatory networks.	2008	the [matlab] code is a
18174185	java	Automated programming for bioinformatics algorithm deployment.	2008	for most [java] bioinform
18154664	javascript	Userscripts for the life sciences.	2007	ritten in [javascript]. informat
18086686	r	affyGG: computational protocols for genetical genomics with Affymetrix arrays.	2008	s: (i) an [R package] providing
18086686	perl	affyGG: computational protocols for genetical genomics with Affymetrix arrays.	2008	and (ii) [perl] scripts p
18056736	c++	Rfold: an exact algorithm for computing local base pairing probabilities.	2008	the [C++] source co
18056069	java	Automated manipulation of systems biology models using libSBML within Taverna workflows.	2008	nd invoke [java] classes a
18056063	r	Model-based deconvolution of genome-wide DNA binding.	2008	en-source [R package], includin
18042557	mathlab	Estimating parameters and hidden variables in non-linear state-space models based on ODEs for biological networks inference.	2007	[matlab] code avai
18037684	r	RReportGenerator: automatic reports from routine statistical analysis using R.	2008	analysis [using R].
18037683	perl	Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species.	2008	l and the [perl] scripts p
18034891	java	Dendroscope: An interactive viewer for large phylogenetic trees.	2007	ritten in [java] 1.4 and i
18033794	java	Analysis of a Gibbs sampler method for model-based clustering of gene expression data.	2008	ganesh, a [java] package f
18033791	java	PedVizApi: a Java API for the interactive, visual analysis of extended pedigrees.	2008	vizapi: a [java] api for t
18028540	c	Recodon: coalescent simulation of coding DNA sequences with recombination, migration and demography.	2007	ecodon is [written in C], can run
18025006	r	Estimating node degree in bait-prey graphs.	2008	rough the [Bioconductor] project (
18024976	r	GlobalANCOVA: exploration and assessment of gene group effects.	2008	ttp://www.[Bioconductor].org) offe
18024975	mathlab	Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting.	2008	tirelief. [matlab] source co
18024972	mathlab	A profile-based deterministic sequential Monte Carlo algorithm for motif discovery.	2008	[matlab] code is a
18024473	r	Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R.	2008	tree cut [R package] that impl
18006550	r	GEIGER: investigating evolutionary radiations.	2008	en in the [R language], to descr
18006546	c++	GWAsimulator: a rapid whole-genome simulation program.	2008	the [C++] source co
18005434	r	Novel definition files for human GeneChips based on GeneAnnot.	2007	uidelines [and R] code, cdf
18005402	perl	A general strategy to determine the congruence between a hierarchical and a non-hierarchical classification.	2007	tegies. a [perl] script th
18003646	mathlab	Independent component analysis for the extraction of reliable protein signal profiles from MALDI-TOF mass spectra.	2008	the [matlab] implement
18003643	r	Vbmp: variational Bayesian Multinomial Probit Regression for multi-class classification in R.	2008	bmp is an [R package] for gauss
17997843	r	BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips.	2007	conductor [R package] that impl
17996092	java	An open source infrastructure for managing knowledge and finding potential collaborators in a domain-specific subset of PubMed, with an example from human genome epidemiology.	2007	esign and [java] as a plat
17989096	r	Rintact: enabling computational analysis of molecular interaction data from the IntAct repository.	2008	intact, a [Bioconductor] package t
17989094	java	Hierarchical tree snipping: clustering guided by prior knowledge.	2007	a [java] package i
17977888	python	Moment invariants as shape recognition technique for comparing protein binding sites.	2007	[python] code is a
17977884	mathlab	Ensemble learning of genetic networks from time-series expression data.	2007	the [matlab] codes are
17977882	java	PfamAlyzer: domain-centric homology search.	2007	yzer is a [java] applet th
17947255	c++	i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles.	2008	tains the [C++] source co
17947255	perl	i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles.	2008	s various [perl] scripts a
17941985	java	Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing.	2007	mented in [java]. the soft
17939871	mathlab	Local Renyi entropic profiles of DNA sequences.	2007	eloped in [matlab] m-code, t
17937818	java	MindSeer: a portable and extensible tool for visualization of structural and functional neuroimaging data.	2007	lization, [java] and java3
17937790	r	Large scale statistical inference of signaling pathways from RNAi and microarray data.	2007	from the [Bioconductor] homepage.
17933854	r	MDQC: a new quality assessment method for microarrays based on quality control reports.	2007	able from [Bioconductor].
17921494	java	Biclustering as a method for RNA local multiple sequence alignment.	2007	mented in [java]. source c
17921491	c++	Improved BLAST searches using longer words for protein seeding.	2007	cbi c and [C++] toolkit c
17921172	r	I/NI-calls for the exclusion of non-informative genes: a highly effective filtering tool for microarray data.	2007	ed in the [R package] farms (ww
17906332	r	A microarray analysis for differential gene expression in the soybean genome using Bioconductor and R.	2007	conductor [and R].
17903289	r	Graphs in molecular biology.	2007	rough the [Bioconductor] project a
17900369	r	A latent variable approach for meta-analysis of gene expression data from multiple microarray experiments.	2007	ble as an [R package], metaarra
17895273	perl	TandTRAQ: an open-source tool for integrated protein identification and quantitation.	2007	tandtraq [perl] scripts a
17893085	java	TreeSnatcher: coding trees from images.	2007	ui-driven [java] applicati
17881408	r	Moderated statistical tests for assessing differences in tag abundance.	2007	an [R package] can be ac
17880681	c	A cross-species alignment tool (CAT).	2007	plemented [using C] scripts a
17877799	mathlab	A framework for significance analysis of gene expression data using dimension reduction methods.	2007	le, and a [matlab] toolbox (
17875544	r	oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language.	2007	liar with [R language].
17872912	mathlab	Graph-based consensus clustering for class discovery from gene expression data.	2007	[matlab] source co
17855420	javascript	AVIS: AJAX viewer of interactive signaling networks.	2007	nchronous [javascript] with xml)
17855418	java	Cyto-Sim: a formal language model and stochastic simulator of membrane-enclosed biochemical processes.	2007	and-alone [java] program v
17855418	mathlab	Cyto-Sim: a formal language model and stochastic simulator of membrane-enclosed biochemical processes.	2007	sbml and [matlab] m-files.
17854506	javascript	OntologyWidget - a reusable, embeddable widget for easily locating ontology terms.	2007	nchronous [javascript] and xml)
17846036	c++	Clustal W and Clustal X version 2.0.	2007	ritten in [C++]. this wil
17846035	c++	A genotype calling algorithm for the Illumina BeadArray platform.	2007	the [C++] executabl
17827205	mathlab	Exploiting sample variability to enhance multivariate analysis of microarray data.	2007	[matlab] script fi
17768165	r	An error model for protein quantification.	2007	matlab [and R] code is a
17768165	mathlab	An error model for protein quantification.	2007	[matlab] and r cod
17767709	r	GeneSrF and varSelRF: a web-based tool and R package for gene selection and classification using random forest.	2007	tool and [R package] for gene
17725829	java	Integrated network reconstruction, visualization and analysis using YANAsquare.	2007	ackage in [java]. it is fu
17725821	perl	MaxAlign: maximizing usable data in an alignment.	2007	able as a [perl] stand-alo
17720985	mathlab	Metal reduction kinetics in Shewanella.	2007	mented in [matlab]. it consi
17720982	r	A comparison of background correction methods for two-colour microarrays.	2007	le in the [R package] limma (sm
17716377	java	Protein structural similarity search by Ramachandran codes.	2007	and-alone [java] program t
17683598	java	TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy.	2007	ritten in [java] as a plug
17683565	r	Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data.	2007	ithin the [R package] gimmr whi
17678535	perl	PepBank--a database of peptides based on sequence text mining and public peptide data sources.	2007	ell as on [CPAN] (http://w
17660206	r	Robust smooth segmentation approach for array CGH data analysis.	2007	the [R package] smoothseg
17660205	r	sMOL Explorer: an open source, web-enabled database and exploration tool for Small MOLecules datasets.	2007	from weka [and R] packages
17655753	r	msBayes: pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation.	2007	several c [and R] programs
17655753	perl	msBayes: pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation.	2007	un with a [perl] front-en
17646351	java	Homology search for genes.	2007	the [java] implement
17646350	java	In search of lost introns.	2007	the [java] implement
17646338	r	From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensis.	2007	grams are [written in R] and avail
17646331	java	Continuous hidden process model for time series expression experiments.	2007	a [java] implement
17646320	java	Functional annotation of regulatory pathways.	2007	mented in [java] and is av
17646311	r	Nested effects models for high-dimensional phenotyping screens.	2007	le in the [R package] 'nem' fro
17646288	mathlab	Kernel-based data fusion for gene prioritization.	2007	the [matlab] code used
17644558	java	GSEA-P: a desktop application for Gene Set Enrichment Analysis.	2007	on of the [java] based sof
17626633	java	A novel ensemble learning method for de novo computational identification of DNA binding sites.	2007	nterface, [java] source co
17623703	c++	HMMoC--a compiler for hidden Markov models.	2007	efficient [C++] implement
17623700	r	RefPlus: an R package extending the RMA Algorithm.	2007	fplus: an [R package] extending
17605777	mathlab	Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data.	2007	lable for [matlab] and will
17599937	perl	CASVM: web server for SVM-based prediction of caspase substrates cleavage sites.	2007	ritten in [perl] and hoste
17599935	mathlab	Improving gene quantification by adjustable spot-image restoration.	2007	mented in [matlab] (the math
17599926	python	QPRIMER: a quick web-based application for designing conserved PCR primers from multigenome alignments.	2007	pygr (the [python] graph dat
17594490	java	Constructing a meaningful evolutionary average at the phylogenetic center of mass.	2007	design. a [java] implement
17594490	r	Constructing a meaningful evolutionary average at the phylogenetic center of mass.	2007	atistical [language r].
17594472	r	Ringo--an R/Bioconductor package for analyzing ChIP-chip readouts.	2007	en-source [R package] ringo tha
17586828	r	beadarray: R classes and methods for Illumina bead-based data.	2007	from the [Bioconductor] web page
17586826	mathlab	BiVisu: software tool for bicluster detection and visualization.	2007	eloped in [matlab] and is av
17586549	java	Evaporative cooling feature selection for genotypic data involving interactions.	2007	ritten in [java], is freel
17586546	r	Annotation-based distance measures for patient subgroup discovery in clinical microarray studies.	2007	ovide the [R package] adsplit a
17586543	r	Multivariate correlation estimator for inferring functional relationships from replicated genome-wide data.	2007	ted in an [R package] 'correp'
17584939	mathlab	Precise protein quantification based on peptide quantification using iTRAQ.	2007	2.2. the [matlab] scripts o
17584922	python	Three-Dimensional Phylogeny Explorer: distinguishing paralogs, lateral transfer, and violation of molecular clock assumption with 3D visualization.	2007	cientific [python] to genera
17559666	perl	Bio::NEXUS: a Perl API for the NEXUS format for comparative biological data.	2007	:nexus: a [perl] api for t
17553857	r	Predicting survival from microarray data--a comparative study.	2007	matlab [and R] code for
17553857	mathlab	Predicting survival from microarray data--a comparative study.	2007	[matlab] and r cod
17550911	java	Finding cis-regulatory modules in Drosophila using phylogenetic hidden Markov models.	2007	available [java] program:
17545183	java	OBO-Edit--an ontology editor for biologists.	2007	mented in [java], obo-edit
17540683	c++	Simple and fast alignment of metabolic pathways by exploiting local diversity.	2007	mented in [C++] as a user
17540682	mathlab	Bayesian modelling of shared gene function.	2007	ement and [matlab] code are
17537755	python	PALMA: mRNA to genome alignments using large margin algorithms.	2007	n c++ and [python] are avail
17537755	c++	PALMA: mRNA to genome alignments using large margin algorithms.	2007	mented in [C++] and pytho
17537750	java	StrBioLib: a Java library for development of custom computational structural biology applications.	2007	biolib: a [java] library f
17519250	r	Discovering gene expression patterns in time course microarray experiments by ANOVA-SCA.	2007	atistical [language r] and is av
17519247	c++	The evolutionary forest algorithm.	2007	a [C++] implement
17519018	r	GOSim--an R-package for computation of information theoretic GO similarities between terms and gene products.	2007	ithin the [CRAN] project.
17510172	perl	Error detection in SNP data by considering the likelihood of recombinational history implied by three-site combinations.	2007	the [perl] script im
17496320	r	GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor.	2007	(geo) and [Bioconductor].
17496317	java	OBO to OWL: a protege OWL tab to read/save OBO ontologies.	2007	verter, a [java] tool to c
17495999	r	WilcoxCV: an R package for fast variable selection in cross-validation.	2007	coxcv: an [R package] for fast
17495998	java	MutationFinder: a high-performance system for extracting point mutation mentions from text.	2007	perl and [java]. mutation
17495998	python	MutationFinder: a high-performance system for extracting point mutation mentions from text.	2007	ilable in [python], perl and
17495998	perl	MutationFinder: a high-performance system for extracting point mutation mentions from text.	2007	n python, [perl] and java.
17495997	mathlab	PLMaddon: a power-law module for the Matlab SBToolbox.	2007	e for the [matlab] sbtoolbox
17495995	java	Nucleotide composition string selection in HIV-1 subtyping using whole genomes.	2007	the [java] executabl
17488757	c++	Madeline 2.0 PDE: a new program for local and web-based pedigree drawing.	2007	-oriented [C++] and relea
17485432	r	CALIB: a Bioconductor package for estimating absolute expression levels from two-color microarray data.	2007	calib: a [Bioconductor] package f
17485430	r	Assessment of survival prediction models based on microarray data.	2007	ted in an [R package] called pe
17483508	mathlab	Phenotypic clustering of yeast mutants based on kinetochore microtubule dynamics.	2007	ritten in [matlab], can be d
17483503	java	PQuad--a visual analysis platform for proteomic data exploration of microbial organisms.	2007	requires [java] 1.5 and h
17477871	r	A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array.	2007	ted in an [R package] faseg, wh
17470480	java	SPACER: identification of cis-regulatory elements with non-contiguous critical residues.	2007	a [java] 1.4 imple
17468121	mathlab	Alignment of molecular networks by integer quadratic programming.	2007	[matlab] code and
17463028	mathlab	Identifying the biologically relevant gene categories based on gene expression and biological data: an example on prostate cancer.	2007	e code in [matlab] is access
17463026	java	iHMMune-align: hidden Markov model-based alignment and identification of germline genes in rearranged immunoglobulin gene sequences.	2007	-platform [java] executabl
17459965	perl	TOPD/FMTS: a new software to compare phylogenetic trees.	2007	the [perl] source co
17459963	c++	GENOME: a rapid coalescent-based whole genome simulator.	2007	ogram and [C++] source co
17459961	c++	Murlet: a practical multiple alignment tool for structural RNA sequences.	2007	the [C++] source co
17445272	perl	CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L.) methylation filtered genomic genespace sequences.	2007	using the [perl] programmi
17445272	javascript	CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L.) methylation filtered genomic genespace sequences.	2007	mented in [javascript] and perl
17430557	perl	ESTuber db: an online database for Tuber borchii EST sequences.	2007	developed [perl] scripts.
17428344	python	Flexible mapping of homology onto structure with homolmapper.	2007	ritten in [python] to ensure
17425803	perl	BranchClust: a phylogenetic algorithm for selecting gene families.	2007	mented in [perl] with the
17394657	r	Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: high-resolution annotation for microarrays.	2007	ible with [Bioconductor], affymetr
17392333	java	Cyclone: java-based querying and computing with Pathway/Genome databases.	2007	xtensible [java] object ap
17392331	mathlab	Modeling sequence-sequence interactions for drug response.	2007	ritten in [matlab] can be do
17389034	java	Modeling biochemical transformation processes and information processing with Narrator.	2007	mented as [java] software
17384430	java	MPP: a microarray-to-phylogeny pipeline for analysis of gene and marker content datasets.	2007	mpp is a [java] applicati
17384428	java	Semantic Web Service provision: a realistic framework for Bioinformatics programmers.	2007	existing [java] applicati
17384426	perl	GoSh: a web-based database for goat and sheep EST sequences.	2007	e tags. a [perl] pipeline
17384020	r	IlluminaGUI: graphical user interface for analyzing gene expression data generated on the Illumina platform.	2007	nted as a [R package] based on
17384017	mathlab	SBML export interface for the systems biology toolbox for MATLAB.	2007	olbox for [matlab].
17384016	java	Mediante: a web-based microarray data manager.	2007	oped as a [j2ee] three-tie
17379692	r	Domain-enhanced analysis of microarray data using GO annotations.	2007	e in r as [Bioconductor] packages,
17346331	java	Orthology prediction at scalable resolution by phylogenetic tree analysis.	2007	eliminary [java] version o
17344241	r	pcaMethods--a bioconductor package providing PCA methods for incomplete data.	2007	ethods--a [Bioconductor] package p
17344240	r	Codelink: an R package for analysis of GE healthcare gene expression bioarrays.	2007	elink: an [R package] for analy
17344233	java	BioGuideSRS: querying multiple sources with a user-centric perspective.	2007	stem with [java] 5.0.
17341494	java	Comparative annotation of viral genomes with non-conserved gene structure.	2007	the [java] code is a
17341299	java	SBMLeditor: effective creation of models in the Systems Biology Markup language (SBML).	2007	ritten in [java] using jco
17332022	perl	NucPred--predicting nuclear localization of proteins.	2007	tion, the [perl] code is m
17332019	c++	COBALT: constraint-based alignment tool for multiple protein sequences.	2007	the ncbi [C++] toolkit.
17324941	java	Multiple structural alignment and clustering of RNA sequences.	2007	mented in [java] and is, a
17324941	perl	Multiple structural alignment and clustering of RNA sequences.	2007	ompanying [perl] scripts,
17324940	java	Enabling high-throughput data management for systems biology: the Bioinformatics Resource Manager.	2007	ped using [java] and other
17316423	java	Bioclipse: an open source workbench for chemo- and bioinformatics.	2007	ritten in [java] and based
17309895	java	Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation.	2007	en-source [java] plugin fo
17308338	java	A new JAVA interface implementation of THESIAS: testing haplotype effects in association studies.	2007	a new [java] interface
17282999	c++	Assessment of the probabilities for evolutionary structural changes in protein folds.	2007	system in [C++] and using
17280615	java	NeuroTerrain--a client-server system for browsing 3D biomedical image data sets.	2007	of a thin [java] client bu
17280615	c++	NeuroTerrain--a client-server system for browsing 3D biomedical image data sets.	2007	n in ansi [C++]. the java
17277335	c	Hardware acceleration of processing of mass spectrometric data for proteomics.	2007	algorithm [written in C], running
17267438	mathlab	An ensemble approach to microarray data-based gene prioritization after missing value imputation.	2007	the [matlab] codes are
17267436	r	SNPassoc: an R package to perform whole genome association studies.	2007	assoc: an [R package] to perfor
17244370	java	GraphDNA: a Java program for graphical display of DNA composition analyses.	2007	aphdna: a [java] program f
17242030	c++	SatDNA Analyzer: a computing tool for satellite-DNA evolutionary analysis.	2007	mented in [C++], for the
17237105	c++	A comparative genome approach to marker ordering.	2007	ftware in [C++], includin
17237103	c++	Simultaneous alignment and annotation of cis-regulatory regions.	2007	ine based [C++] implement
17237103	perl	Simultaneous alignment and annotation of cis-regulatory regions.	2007	e provide [perl] scripts f
17237101	c++	Tandem repeats over the edit distance.	2007	mented in [C++], and the
17237073	perl	ProServer: a simple, extensible Perl DAS server.	2007	xtensible [perl] das serve
17237072	python	Biskit--a software platform for structural bioinformatics.	2007	-oriented [python] library t
17237071	mathlab	SBaddon: high performance simulation for the Systems Biology Toolbox for MATLAB.	2007	olbox for [matlab].
17237067	mathlab	Inferring pairwise regulatory relationships from multiple time series datasets.	2007	[matlab] implement
17237065	mathlab	Peak selection from MALDI-TOF mass spectra using ant colony optimization.	2007	erial and [matlab] scripts t
17237063	c++	Compressed suffix tree--a basis for genome-scale sequence analysis.	2007	the [C++] implement
17237060	mathlab	Quick calculation for sample size while controlling false discovery rate with application to microarray analysis.	2007	a [matlab] code impl
17237056	java	The ESID Online Database network.	2007	based on [java] 2 enterpr
17237045	mathlab	Genomic characterization of multiple clinical phenotypes of cancer using multivariate linear regression models.	2007	sas and [matlab] codes are
17237038	r	R/qtlbim: QTL with Bayesian Interval Mapping in experimental crosses.	2007	able from [CRAN].r-project
17234643	r	A faster circular binary segmentation algorithm for the analysis of array CGH data.	2007	ge of the [Bioconductor] project.
17234637	r	snp.plotter: an R-based SNP/haplotype association and linkage disequilibrium plotting package.	2007	developed [R package] which pro
17233908	java	AYUMS: an algorithm for completely automatic quantitation based on LC-MS/MS proteome data and its application to the analysis of signal transduction.	2007	ped using [java] and runs
17224057	r	Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips.	2007	etrix and [Bioconductor] in early
17217518	java	SVM Classifier - a comprehensive java interface for support vector machine classification of microarray data.	2006	rehensive [java] interface
17217507	c++	Parallelization of multicategory support vector machines (PMC-SVM) for classifying microarray data.	2006	g mpi and [C++] libraries
17204461	r	SNPchip: R classes and methods for SNP array data.	2007	tion. the [R package] snpchip c
17204155	c++	FLAME, a novel fuzzy clustering method for the analysis of DNA microarray data.	2007	hms, in a [C++] software
17199898	c++	TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences.	2007	, and the [C++] and perl
17199898	perl	TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences.	2007	e c++ and [perl] sources o
17182699	c++	URec: a system for unrooted reconciliation.	2007	mented in [C++] and can b
17182698	c++	Robust prediction of consensus secondary structures using averaged base pairing probability matrices.	2007	the [C++] source co
17166856	r	Segmentation and intensity estimation of microarray images using a gamma-t mixture model.	2007	mentation [R language] softwares
17166856	mathlab	Segmentation and intensity estimation of microarray images using a gamma-t mixture model.	2007	mented in [matlab]. the matl
17166289	java	The NeuARt II system: a viewing tool for neuroanatomical data based on published neuroanatomical atlases.	2006	') in the [java] language
17158515	mathlab	Quantitative performance metrics for robustness in circadian rhythms.	2007	orithm in [matlab] (mathwork
17158513	r	GGtools: analysis of genetics of gene expression in bioconductor.	2007	ession in [Bioconductor].
17145740	c	cBrother: relaxing parental tree assumptions for Bayesian recombination detection.	2007	s a novel [C language] implement
17142814	java	The automation of Nested Clade Phylogeographic Analysis.	2007	ritten in [java] and requi
17138590	java	MotifScorer: using a compendium of microarrays to identify regulatory motifs.	2007	ritten in [java] and matla
17138590	mathlab	MotifScorer: using a compendium of microarrays to identify regulatory motifs.	2007	java and [matlab], manual a
17138589	java	Visualization of genomic aberrations using Affymetrix SNP arrays.	2007	dependent [java] applicati
17138585	java	BioNetBuilder: automatic integration of biological networks.	2007	able as a [java] webstart,
17130137	mathlab	Improved breast cancer prognosis through the combination of clinical and genetic markers.	2007	e.com and [matlab] codes are
17127677	r	Mosclust: a software library for discovering significant structures in bio-molecular data.	2007	the [R package] mosclust
17121773	mathlab	PrepMS: TOF MS data graphical preprocessing tool.	2007	files and [matlab] toolbox a
17118131	c++	Permutation test for periodicity in short time series data.	2006	a set of [C++] programs
17116249	r	CoXpress: differential co-expression in gene expression data.	2006	press, an [R package] that allo
17105719	mathlab	Detecting protein dissimilarities in multiple alignments using Bayesian variable selection.	2007	the [matlab] code for
17101042	java	4SALE--a tool for synchronous RNA sequence and secondary structure alignment and editing.	2006	ritten in [java] and there
17098774	r	Using GOstats to test gene lists for GO term association.	2007	ble as an [R package] from the
17095514	c	Pattern locator: a new tool for finding local sequence patterns in genomic DNA sequences.	2006	e code is [written in C] and distr
17092991	java	Modular organization of protein interaction networks.	2007	orithm. a [java] program,
17092990	r	Odds ratio based multifactor-dimensionality reduction method for detecting gene-gene interactions.	2007	e program [written in R] is availa
17087823	java	XML schemas for common bioinformatic data types and their application in workflow systems.	2006	them in a [java] library (
17077099	java	Towards clustering of incomplete microarray data without the use of imputation.	2007	ped using [java] language,
17068091	c++	Adding sequence context to a Markov background model improves the identification of regulatory elements.	2006	our [C++] program i
17064411	perl	CAFTAN: a tool for fast mapping, and quality assessment of cDNAs.	2006	ritten in [perl] and in a
17060354	java	Prediction of oxidoreductase-catalyzed reactions based on atomic properties of metabolites.	2006	ses via a [java] program a
17059604	perl	SNP-PHAGE--High throughput SNP discovery pipeline.	2006	ritten in [perl] and uses
17059595	r	Goulphar: rapid access and expertise for standard two-color microarray normalization methods.	2006	using the [R language] and envir
17054794	java	Java GUI for InterProScan (JIPS): a tool to help process multiple InterProScans and perform ortholog analysis.	2006	[java] gui for i
17054788	java	inGeno--an integrated genome and ortholog viewer for improved genome to genome comparisons.	2006	ritten in [java] with bioj
17046977	java	MetaQuant: a tool for the automatic quantification of GC/MS-based metabolome data.	2006	ritten in [java] and is av
17038344	c++	Parameter estimation using Simulated Annealing for S-system models of biochemical networks.	2007	ritten in [C++] is availa
17038193	java	A Fisheye Viewer for microarray-based gene expression data.	2006	mented in [java] so that i
17038191	java	MIMOX: a web tool for phage display based epitope mapping.	2006	view as a [java] applet to
17038191	perl	MIMOX: a web tool for phage display based epitope mapping.	2006	coded in [perl] using mod
17032677	java	ChromoScan: a scan statistic application for identifying chromosomal regions in genomic studies.	2006	ements. a [java] graphic u
17021156	r	P2BAT: a massive parallel implementation of PBAT for genome-wide association studies in R.	2006	le as the [R package] 'pbatr' w
17005537	r	BNArray: an R package for constructing gene regulatory networks from microarray data by using Bayesian network.	2006	array: an [R package] for const
17005535	perl	CAPS: coevolution analysis using protein sequences.	2006	aps) is a [perl] based sof
17000750	c++	Software for dynamic analysis of tracer-based metabolomic data: estimation of metabolic fluxes and their statistical analysis.	2006	the [C++] applicati
16982708	r	RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis.	2006	nkprod: a [Bioconductor] package f
16966362	mathlab	Probabilistic inference of transcription factor concentrations and gene-specific regulatory activities.	2006	[matlab] code is a
16966359	python	SCAssign: a sparky extension for the NMR resonance assignment of aliphatic side-chains of uniformly 13C,15N-labeled large proteins.	2006	ritten in [python] to assist
16954144	java	SEBINI: Software Environment for BIological Network Inference.	2006	html. the [java] source co
16953879	java	A database application for pre-processing, storage and comparison of mass spectra derived from patients and controls.	2006	ritten in [java], 2) a mys
16940322	r	Bio3d: an R package for the comparative analysis of protein structures.	2006	bio3d: an [R package] for the c
16928738	c++	MARD: a new method to detect differential gene expression in treatment-control time courses.	2006	coded in [C++] and is av
16895932	r	COPA--cancer outlier profile analysis.	2006	pa) in an [R package] (that we
16895923	c++	Few crucial links assure checkpoint efficiency in the yeast cell-cycle network.	2006	[C++] source co
16882649	c++	Nemo: an evolutionary and population genetics programming framework.	2006	as both a [C++] programmi
16882648	python	PYCHEM: a multivariate analysis package for python.	2006	ckage for [python].
16882648	mathlab	PYCHEM: a multivariate analysis package for python.	2006	ools like [matlab], pychem 2
16882647	r	Reliable gene signatures for microarray classification: assessment of stability and performance.	2006	[R package] at http:/
16877754	c++	General framework for developing and evaluating database scoring algorithms using the TANDEM search engine.	2006	ritten in [C++].
16877753	r	Variance stabilization and normalization for one-color microarray data using a data-driven multiscale approach.	2006	the [R package] of the da
16877752	r	Partition resampling and extrapolation averaging: approximation methods for quantifying gene expression in large numbers of short oligonucleotide arrays.	2006	ent as an [R package] for the b
16873522	mathlab	AClAP, Autonomous hierarchical agglomerative Cluster Analysis based protocol to partition conformational datasets.	2006	nted in a [matlab] metalangu
16873504	mathlab	Integrating copy number polymorphisms into array CGH analysis using a robust HMM.	2006	ritten in [matlab] is availa
16873460	java	Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles.	2006	ctave and [java] (with a g
16870933	java	JVirGel 2.0: computational prediction of proteomes separated via two-dimensional gel electrophoresis under consideration of membrane and secreted proteins.	2006	dependent [java] version a
16864592	r	arrayQCplot: software for checking the quality of microarray data.	2006	developed [using R] and provi
16845144	mathlab	Bayesian variable selection for the analysis of microarray data with censored outcomes.	2006	the [matlab] code for
16844712	r	OrderedList--a bioconductor package for detecting similarity in ordered gene lists.	2006	edlist--a [Bioconductor] package f
16844709	perl	SynView: a GBrowse-compatible approach to visualizing comparative genome data.	2006	ritten in [perl] and runs
16844707	java	CART variance stabilization and regularization for high-throughput genomic data.	2006	ithin the [java] software
16844704	mathlab	Gene selection in cancer classification using sparse logistic regression with Bayesian regularization.	2006	a [matlab] implement
16837522	mathlab	Remote homology detection based on oligomer distances.	2006	e/thomas. [matlab] code for
16824223	r	AMDA: an R package for the automated microarray data analysis.	2006	amda: an [R package] for the a
16820431	java	VAMP: visualization and analysis of array-CGH, transcriptome and other molecular profiles.	2006	ritten in [java]. it can b
16820430	mathlab	Ribostral: an RNA 3D alignment analyzer and viewer based on basepair isostericities.	2006	form with [matlab] 7.1 (sp3)
16820429	r	Probe-level measurement error improves accuracy in detecting differential gene expression.	2006	ted in an [R package] pplr. the
16820429	mathlab	Probe-level measurement error improves accuracy in detecting differential gene expression.	2006	mented in [matlab]. both sof
16820428	r	Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching.	2006	le in the [Bioconductor] project.
16817977	java	PROMPT: a protein mapping and comparison tool.	2006	ty of the [java] applicati
16809393	c++	An iterative refinement algorithm for consistency based multiple structural alignment methods.	2006	the [C++] code of t
16809388	java	ET viewer: an application for predicting and visualizing functional sites in protein structures.	2006	ted using [java] to run ac
16809386	r	Pathway analysis using random forests classification and regression.	2006	urce code [written in R] is availa
16792813	r	PSMIX: an R package for population structure inference via maximum likelihood method.	2006	psmix: an [R package] for popul
16790057	perl	AgdbNet - antigen sequence database software for bacterial typing.	2006	rsed by a [perl] cgi scrip
16787977	mathlab	A lock-and-key model for protein-protein interactions.	2006	rithm (in [matlab] format) i
16787976	python	Cleaver: software for identifying taxon specific restriction endonuclease recognition sites.	2006	that have [python] 2.3 and n
16787969	r	Transcript mapping with high-density oligonucleotide tiling arrays.	2006	[R package] tilingarr
16782726	java	Building chromosome-wide LD maps.	2006	coded in [java], which ru
16782725	java	JCell--a Java-based framework for inferring regulatory networks from time series data.	2006	is a pure [java] applicati
16777905	r	Robust estimation of the false discovery rate.	2006	of s-plus [and R] routines
16766560	java	JADE: a distributed Java application for deleterious genomic mutation (DGM) estimation.	2006	stributed [java] applicati
16766557	java	SeqVis: visualization of compositional heterogeneity in large alignments of nucleotides.	2006	seqvis, a [java] applicati
16766556	mathlab	Transcriptome network component analysis with limited microarray data.	2006	olbox for [matlab] is availa
16762054	java	Cell_motility: a cross-platform, open source application for the study of cell motion paths.	2006	en source [java] applicati
16740163	java	AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis.	2006	ritten in [java] we have p
16740163	c	AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis.	2006	g program [written in C] with a us
16731697	mathlab	Metatool 5.0: fast and flexible elementary modes analysis.	2006	octave or [matlab] environme
16717070	c	NETGEN: generating phylogenetic networks with diploid hybrids.	2006	netgen is [written in C] and is av
16716215	r	Spatial normalization of array-CGH data.	2006	ed in the [R package] manor (mi
16709589	mathlab	Independent component analysis-based penalized discriminant method for tumor classification using gene expression data.	2006	[matlab] scripts a
16709588	java	Combo: a whole genome comparative browser.	2006	ritten in [java], runs on
16705015	r	Combining multiple microarrays in the presence of controlling variables.	2006	programs [written in R] will be e
16700920	java	Bounded search for de novo identification of degenerate cis-regulatory elements.	2006	ethods. a [java] implement
16682424	r	PACK: Profile Analysis using Clustering and Kurtosis to find molecular classifiers in cancer.	2006	from (www.[CRAN].r-project
16675467	fortran	A mixture model with random-effects components for clustering correlated gene-expression profiles.	2006	a [fortran] program b
16643673	mathlab	PDA: Pooled DNA analyzer.	2006	with the [matlab] language,
16640789	java	JColorGrid: software for the visualization of biological measurements.	2006	orgrid, a [java] library a
16638137	java	RNAmute: RNA secondary structure mutation analysis tool.	2006	teractive [java] applicati
16632491	c++	GeneRecon--a coalescent based tool for fine-scale association mapping.	2006	ritten in [C++] and schem
16632490	mathlab	A probabilistic dynamical model for quantitative inference of the regulatory mechanism of transcription.	2006	[matlab] code is a
16630347	java	Exploration of biological network centralities with CentiBiN.	2006	rsions: a [java] web start
16623940	r	Assessment of the relationship between pre-chip and post-chip quality measures for Affymetrix GeneChip expression data.	2006	p and the [Bioconductor] packages
16611354	mathlab	Integrative investigation of metabolic and transcriptomic data.	2006	oolbox in [matlab].
16600045	java	An interactive tool for visualization of relationships between gene expression profiles.	2006	ritten in [java], treebuil
16600027	java	AbMiner: a bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies.	2006	rammed in [java].
16595561	java	ProMAT: protein microarray analysis tool.	2006	en-source [java] and r cod
16595561	r	ProMAT: protein microarray analysis tool.	2006	urce java [and R] code.
16595560	r	Pvclust: an R package for assessing the uncertainty in hierarchical clustering.	2006	clust: an [R package] for asses
16594991	c++	Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics.	2006	a set of [C++] libraries
16574698	r	SScore: an R package for detecting differential gene expression without gene expression summaries.	2006	score: an [R package] for detec
16574696	mathlab	SBMLToolbox: an SBML toolbox for MATLAB users.	2006	olbox for [matlab] users.
16569235	java	The Gaggle: an open-source software system for integrating bioinformatics software and data sources.	2006	en-source [java] software
16556315	java	BioWarehouse: a bioinformatics database warehouse toolkit.	2006	the c and [java] languages
16551664	java	BicAT: a biclustering analysis toolbox.	2006	tems. the [java] source co
16551355	mathlab	Unraveling condition specific gene transcriptional regulatory networks in Saccharomyces cerevisiae.	2006	on of the [matlab] implement
16542435	java	Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models.	2006	ritten in [java] and is pu
16539707	mathlab	mGrid: a load-balanced distributed computing environment for the remote execution of the user-defined Matlab code.	2006	r-defined [matlab] code.
16526950	r	An unsupervised classification scheme for improving predictions of prokaryotic TIS.	2006	udomallei [and R]. solanace
16522668	java	MACGT: multi-dimensional automated clustering genotyping tool for analysis of microarray-based mini-sequencing data.	2006	cgt) is a [java] applicati
16522212	java	MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools.	2006	) or as a [java] graphical
16522212	perl	MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools.	2006	tabase, a [perl] pipeline,
16519817	java	VANTED: a system for advanced data analysis and visualization in the context of biological networks.	2006	nted as a [java] web start
16510496	r	GALGO: an R package for multivariate variable selection using genetic algorithms.	2006	galgo: an [R package] for multi
16507094	java	The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries.	2006	a sample [java] client to
16504125	mathlab	Multiscale Hy3S: hybrid stochastic simulation for supercomputers.	2006	ritten in [matlab], to help
16492684	r	Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences.	2006	programs [written in R] to do the
16473875	perl	Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support.	2006	ritten in [perl] using ope
16473874	r	A new summarization method for Affymetrix probe level data.	2006	the farms [R package] is availa
16469097	java	HotSwap for bioinformatics: a STRAP tutorial.	2006	using the [java] hotswap t
16466584	java	JLIN: a java based linkage disequilibrium plotter.	2006	jlin: a [java] based lin
16466568	java	BAMarraytrade mark: Java software for Bayesian analysis of variance for microarray data.	2006	ade mark: [java] software
16464251	java	PathSys: integrating molecular interaction graphs for systems biology.	2006	able as a [java] web start
16455752	r	affylmGUI: a graphical user interface for linear modeling of single channel microarray data.	2006	gui is an [R package] freely av
16452111	perl	MAMMOT--a set of tools for the design, management and visualization of genomic tiling arrays.	2006	ection of [perl] and php s
16441875	perl	Querying the public databases for sequences using complex keywords contained in the feature lines.	2006	specific [perl] scripts t
16434446	java	ProteomeCommons.org JAF: reference information and tools for proteomics.	2006	nces. the [java] analysis
16418234	java	Panta rhei (QAlign2): an open graphical environment for sequence analysis.	2006	s and the [java] source co
16410320	r	Comparison of Affymetrix GeneChip expression measures.	2006	rt of the [Bioconductor] project (
16410318	java	Maximum likelihood estimates of allele frequencies and error rates from samples of related individuals by gene counting.	2006	the [java] classes a
16403793	mathlab	Using a state-space model with hidden variables to infer transcription factor activities.	2006	data and [matlab] code will
16403221	python	A high level interface to SCOP and ASTRAL implemented in python.	2006	mented in [python].
16398931	perl	Application of machine learning in SNP discovery.	2006	ritten in [perl] and can b
16397008	perl	ANDY: a general, fault-tolerant tool for database searching on computer clusters.	2006	a set of [perl] programs
16377613	java	Improving missing value estimation in microarray data with gene ontology.	2006	[java] and matla
16377613	mathlab	Improving missing value estimation in microarray data with gene ontology.	2006	java and [matlab] codes are
16377612	python	GenomeDiagram: a python package for the visualization of large-scale genomic data.	2006	iagram: a [python] package f
16371165	r	WebArray: an online platform for microarray data analysis.	2005	ckages in [Bioconductor], need sop
16371163	perl	The Gene Set Builder: collation, curation, and distribution of sets of genes.	2005	eatures a [perl] api (appl
16368771	java	FLOSS: flexible ordered subset analysis for linkage mapping of complex traits.	2006	ritten in [java] for easy
16357032	java	SEAN: SNP prediction and display program utilizing EST sequence clusters.	2006	iction. a [java] viewer is
16357031	java	eQTL Explorer: integrated mining of combined genetic linkage and expression experiments.	2006	ata via a [java] graphical
16351742	perl	ESTree db: a tool for peach functional genomics.	2005	developed [perl] scripts a
16332714	perl	TRAP: automated classification, quantification and annotation of tandemly repeated sequences.	2006	ram, is a [perl] program t
16332708	r	Clusterv: a tool for assessing the reliability of clusters discovered in DNA microarray data.	2006	ent a new [R package] for the a
16332707	python	BALLView: a tool for research and education in molecular modeling.	2006	language [python] it is eas
16332704	java	PubMed Assistant: a biologist-friendly interface for enhanced PubMed search.	2006	veloped a [java] program,
16322049	r	apTreeshape: statistical analysis of phylogenetic tree shape.	2006	hape is a [R package] dedicated
16321157	r	ArrayQuest: a web resource for the analysis of DNA microarray data.	2005	as those [written in R], bioperl
16321157	perl	ArrayQuest: a web resource for the analysis of DNA microarray data.	2005	ten in r, [bioperl] and c++;
16317076	mathlab	Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology.	2006	software [matlab]. the tool
16303798	fortran	Statistical estimation of gene expression using multiple laser scans of microarrays.	2006	[fortran] 90 code f
16293669	java	Gene Time E{chi}pression Warper: a tool for alignment, template matching and visualization of gene expression time series.	2006	the [java] program,
16287941	c++	WindowMasker: window-based masker for sequenced genomes.	2006	the ncbi [C++] toolkit.
16287938	mathlab	Classification of microarray data with factor mixture models.	2006	ritten in [matlab] and avail
16287932	python	An efficient randomized algorithm for contact-based NMR backbone resonance assignment.	2006	dependent [python] code. the
16269418	r	ClaNC: point-and-click software for classifying microarrays to nearest centroids.	2006	ble as an [R package].
16269415	java	LogoBar: bar graph visualization of protein logos with gaps.	2006	obar is a [java] applicati
16269077	java	maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination.	2005	chema and [java] applicati
16257986	mathlab	Classification using functional data analysis for temporal gene expression data.	2006	[matlab] programs
16257984	mathlab	Robust multi-scale clustering of large DNA microarray datasets with the consensus algorithm.	2006	[matlab] source co
16249260	mathlab	Gene selection using support vector machines with non-convex penalty.	2006	[matlab] codes are
16249259	mathlab	Integrating time-course microarray gene expression profiles with cytotoxicity for identification of biomarkers in primary rat hepatocytes exposed to cadmium.	2006	[matlab] source co
16239306	python	ConFind: a robust tool for conserved sequence identification.	2005	requires [python] 2.3, but
16234319	java	A novel algorithm and web-based tool for comparing two alternative phylogenetic trees.	2006	nted as a [java] applet at
16216830	r	The influence of missing value imputation on detection of differentially expressed genes from microarray data.	2005	the [R package] for linim
16204346	r	Sample size determination for the false discovery rate.	2005	ed s-plus [and R] code libr
16204111	c++	RNA secondary structural alignment with conditional random fields.	2005	mented in [C++] is availa
16204098	java	Recovering haplotype structure through recombination and gene conversion.	2005	mented in [java] and are a
16204097	mathlab	Discriminating between rate heterogeneity and interspecific recombination in DNA sequence alignments with phylogenetic factorial hidden Markov models.	2005	nted in a [matlab] package t
16204095	c++	A gamma mixture model better accounts for among site rate heterogeneity.	2005	[C++] source co
16188927	r	HapSim: a simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients.	2005	ble as an [R package] and can b
16188923	java	Medusa: a simple tool for interaction graph analysis.	2005	dusa is a [java] applicati
16188037	c++	SIMPROT: using an empirically determined indel distribution in simulations of protein evolution.	2005	nted in a [C++] program n
16179358	java	Doelan: a solution for quality control monitoring of microarray production.	2005	ritten in [java] and works
16166098	mathlab	RSIR: regularized sliced inverse regression for motif discovery.	2005	[matlab] programs
16159919	mathlab	Analysis of mass spectral serum profiles for biomarker selection.	2005	[matlab] scripts t
16159913	r	A comparison study: applying segmentation to array CGH data for downstream analyses.	2005	ttp://www.[Bioconductor].org
16144805	mathlab	Optimal word sizes for dissimilarity measures and estimation of the degree of dissimilarity between DNA sequences.	2005	mented in [matlab] code, and
16144548	java	Generalizations of Markov model to characterize biological sequences.	2005	mented in [java] and is av
16141249	java	BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing.	2005	ed in the [java] programmi
16141248	r	Network constrained clustering for gene microarray data.	2005	ted in an [R package] genent
16122395	r	stam--a Bioconductor compliant R package for structured analysis of microarray data.	2005	compliant [R package] for struc
16118262	mathlab	DNA microarray data imputation and significance analysis of differential expression.	2005	[matlab] code is a
16118259	java	Modified SIMPSON O(n3) algorithm for the full sibship reconstruction problem.	2005	ritten in [java] is availa
16109746	mathlab	A statistical model providing comprehensive predictions for the mRNA differential display.	2005	mented in [matlab] (the math
16105898	java	MESHI: a new library of Java classes for molecular modeling.	2005	ibrary of [java] classes f
16102175	r	Calibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrants.	2005	rt of the [Bioconductor] package m
16096348	r	ROCR: visualizing classifier performance in R.	2005	atistical [language r]. it featu
16082012	r	BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis.	2005	is a new [Bioconductor] package t
16081474	java	Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research.	2005	lable via [java] web start
16076888	r	Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis.	2005	leaffy: a [Bioconductor] package f
16076886	java	An automated genotyping system for analysis of HIV-1 and other microbial sequences.	2005	ped using [java] programmi
16076886	perl	An automated genotyping system for analysis of HIV-1 and other microbial sequences.	2005	mming and [perl] scripts,
16051675	java	SpA: web-accessible spectratype analysis: data management, statistical analysis and visualization.	2005	rams in a [java] applet an
16046497	mathlab	Automated Microarray Image Analysis Toolbox for MATLAB.	2005	olbox for [matlab].
16045803	r	Evaluation of normalization methods for cDNA microarray data by k-NN classification.	2005	using the [R language] for stati
16042799	perl	CGH-Profiler: data mining based on genomic aberration profiles.	2005	d through [perl] scripts.c
16030074	perl	HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif.	2005	a set of [perl] scripts a
16022740	perl	Approaching the taxonomic affiliation of unidentified sequences in public databases--an example from the mycorrhizal fungi.	2005	a [perl] script pa
16020473	java	MAVisto: a tool for the exploration of network motifs.	2005	arge as a [java] webstart
16020470	r	A tractable probabilistic model for Affymetrix probe-level analysis across multiple chips.	2005	ted in an [R package], which is
16020468	r	goCluster integrates statistical analysis and functional interpretation of microarray expression data.	2005	e via the [Bioconductor] portal at
16011807	r	Normal uniform mixture differential gene expression detection for cDNA microarrays.	2005	case. an [R package] called nu
16011796	java	SeqX: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures.	2005	veloped a [java] tool, cal
16002431	c++	Rapid simulation and analysis of isotopomer distributions using constraints based on enzyme mechanisms: an example from HT29 cancer cells.	2005	also as a [C++] program i
15998662	r	Local modeling of global interactome networks.	2005	nd in the [R package] apcomplex
15994196	perl	SynBrowse: a synteny browser for comparative sequence analysis.	2005	en source [bioperl] modules.
15994194	java	TO-GO: a Java-based Gene Ontology navigation environment.	2005	nted as a [java] applicati
15992409	perl	Prediction of twin-arginine signal peptides.	2005	based on [perl] syntax re
15987530	r	Species-specific analysis of protein sequence motifs using mutual information.	2005	sing perl [and R] as well a
15987530	perl	Species-specific analysis of protein sequence motifs using mutual information.	2005	ice using [perl] and r as
15985178	python	Full cyclic coordinate descent: solving the protein loop closure problem in Calpha space.	2005	f fccd in [python] is availa
15976072	java	ACT: the Artemis Comparison Tool.	2005	ritten in [java] and can r
15972284	java	BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks.	2005	en-source [java] tool to d
15969769	perl	transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences.	2005	en-source [perl] script th
15961495	mathlab	Bayesian neural network approaches to ovarian cancer identification from high-resolution mass spectrometry data.	2005	mented in [matlab], r and ne
15961487	r	Robust classification modeling on microarray data using misclassification penalized posterior.	2005	le at the [Bioconductor] website (
15961469	perl	A systematic approach for comprehensive T-cell epitope discovery using peptide libraries.	2005	s in r or [perl] are avail
15961466	java	High-recall protein entity recognition using a dictionary.	2005	mented in [java]. algorith
15961453	java	Clustering short time series gene expression data.	2005	taining a [java] implement
15961441	java	caBIONet--A .NET wrapper to access and process genomic data stored at the National Cancer Institute's Center for Bioinformatics databases.	2005	veloped a [java] based dat
15961440	java	Querying and computing with BioCyc databases.	2005	perl and [java], and sql
15961440	perl	Querying and computing with BioCyc databases.	2005	for lisp, [perl] and java,
15960857	perl	AutoFACT: an automatic functional annotation and classification tool.	2005	mented in [perl] and runs
15947019	perl	A quantitative determination of multi-protein interactions by the analysis of confocal images using a pixel-by-pixel assessment algorithm.	2005	eloped in [perl] (v. 5.8,
15947017	python	Sarment: Python modules for HMM analysis and partitioning of sequences.	2005	sarment: [python] modules f
15941744	r	Answer to the comments of K. Dobbin, J. Shih and R. Simon on the paper 'Evaluation of the gene-specific dye-bias in cDNA microarray experiments'.	2005	, j. shih [and R]. simon on
15938750	c++	libcov: a C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny.	2005	libcov: a [C++] bioinform
15932904	c++	Statistics of protein library construction.	2005	rface and [C++] source co
15932902	python	PROVAT: a tool for Voronoi tessellation analysis of protein structures and complexes.	2005	a set of [python] scripts t
15910684	c	Genome comparison without alignment using shortest unique substrings.	2005	hulen are [written in C] and avail
15905279	mathlab	Semi-supervised protein classification using cluster kernels.	2005	he spider [matlab] package i
15905277	r	Prediction error estimation: a comparison of resampling methods.	2005	f results [and R] code for
15905276	java	CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data.	2005	the free [java] runtime e
15905274	java	Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure.	2005	using the [java] language
15905273	java	Dasty and UniProt DAS: a perfect pair for protein feature visualization.	2005	ted using [java] and macro
15879451	perl	Fast parsers for Entrez Gene.	2005	larity of [perl] programmi
15860559	java	ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text.	2005	ncludes a [java] applicati
15855247	java	jPHYDIT: a JAVA-based integrated environment for molecular phylogeny of ribosomal RNA sequences.	2005	ydit is a [java] applicati
15845656	r	Donuts, scratches and blanks: robust model-based segmentation of microarray images.	2005	ntributed [R package] mclust fo
15840706	perl	SNPLINK: multipoint linkage analysis of densely distributed SNP data incorporating automated linkage disequilibrium removal.	2005	link is a [perl] script th
15836795	java	MARS: microarray analysis, retrieval, and storage system.	2005	he latest [j2ee] applicati
15829007	r	ProGenExpress: visualization of quantitative data on prokaryotic genomes.	2005	press, an [R package] that allo
15827079	perl	Visualizing profile-profile alignment: pairwise HMM logos.	2005	ownload a [perl] package t
15817693	python	Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary.	2005	and-alone [python] program t
15817692	c++	Stochastic reaction-diffusion simulation with MesoRD.	2005	ritten in [C++] and licen
15817688	r	twilight; a Bioconductor package for estimating the local false discovery rate.	2005	ilight; a [Bioconductor] package f
15817687	c++	pFind: a novel database-searching software system for automated peptide and protein identification via tandem mass spectrometry.	2005	with the [C++] stl, .net
15814553	c++	BEST: binding-site estimation suite of tools.	2005	in qt, a [C++] applicati
15807904	java	CGHPRO -- a comprehensive data analysis tool for array CGH.	2005	and-alone [java] applicati
15804359	c++	Super paramagnetic clustering of protein sequences.	2005	use using [C++] and it is
15802285	fortran	Density guided importance sampling: application to a reduced model of protein folding.	2005	[fortran] code avai
15797915	r	MADE4: an R package for multivariate analysis of gene expression data.	2005	made4: an [R package] for multi
15788106	perl	Wildfire: distributed, Grid-enabled workflow construction and execution.	2005	e such as [perl]. programm
15780146	mathlab	MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution.	2005	oolbox: a [matlab] toolbox f
15769840	java	SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs).	2005	mented by [java] and perl.
15769840	perl	SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs).	2005	java and [perl]. snpnb ca
15757508	java	JAtlasView: a Java atlas-viewer for browsing biomedical 3D images and atlases.	2005	asview: a [java] atlas-vie
15746275	java	Partition-distance via the assignment problem.	2005	ritten in [java] is availa
15723693	java	Atlas - a data warehouse for integrative bioinformatics.	2005	ges: c++, [java], and perl
15723693	c++	Atlas - a data warehouse for integrative bioinformatics.	2005	anguages: [C++], java, an
15723693	perl	Atlas - a data warehouse for integrative bioinformatics.	2005	java, and [perl]. the meth
15713734	fortran	FastContact: rapid estimate of contact and binding free energies.	2005	ritten in [fortran]. the exec
15705654	r	Estimating cancer survival and clinical outcome based on genetic tumor progression scores.	2005	datasets [and R] code for
15699024	fortran	Time accelerated Monte Carlo simulations of biological networks using the binomial tau-leap method.	2005	ion.html. [fortran] 90 code a
15694009	java	The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications.	2005	ritten in [java], thus off
15677704	r	Molecular decomposition of complex clinical phenotypes using biologically structured analysis of microarray data.	2005	compliant [R package]
15673564	r	Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum.	2005	his paper [and R] code for
15673564	mathlab	Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum.	2005	[matlab] scripts t
15671116	mathlab	Investigating metabolite essentiality through genome-scale analysis of Escherichia coli production capabilities.	2005	e form of [matlab] script fi
15671115	perl	TruMatch--a BLAST post-processor that identifies bona fide sequence matches to genome assemblies.	2005	ritten in [perl] and is fr
15657105	r	Testing association of a pathway with survival using gene expression data.	2005	ttp://www.[Bioconductor].org
15657102	r	Use of within-array replicate spots for assessing differential expression in microarray experiments.	2005	from the [CRAN] repositor
15647304	java	AGML Central: web based gel proteomic infrastructure.	2005	tering. a [java] applet vi
15647300	java	Detecting clusters of different geometrical shapes in microarray gene expression data.	2005	ped using [java] language,
15647291	perl	ALOHOMORA: a tool for linkage analysis using 10K SNP array data.	2005	ritten in [perl] and may b
15642112	java	Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases.	2005	used the [java] data obje
15634352	perl	Visualization of comparative genomic analyses by BLAST score ratio.	2005	nted in a [perl] script, c
15613388	java	An enhanced Java graph applet interface for visualizing interactomes.	2005	enhanced [java] graph app
15598833	r	Differential gene expression detection using penalized linear regression models: the improved SAM statistics.	2005	s results [and R] functions
15598829	c++	CARHTA GENE: multipopulation integrated genetic and radiation hybrid mapping.	2005	used as a [C++] library,
15593402	mathlab	CGH-Plotter: MATLAB toolbox for CGH-data analysis.	2003	-plotter: [matlab] toolbox f
15593401	java	GFPE: gene-finding program evaluation.	2003	a set of [java] classes f
15588288	java	ABC: software for interactive browsing of genomic multiple sequence alignment data.	2004	teractive [java] software
15585532	perl	TERMINUS--Telomeric End-Read Mining IN Unassembled Sequences.	2005	a set of [perl] scripts t
15585529	java	RBT--a tool for building refined Buneman trees.	2005	ritten in [java], is avail
15585527	r	OLIN: optimized normalization, visualization and quality testing of two-channel microarray data.	2005	available [R package]. addition
15585059	r	A two-way interface between limited Systems Biology Markup Language and R.	2004	language [and R].
15572472	java	Generalized Venn diagrams: a new method of visualizing complex genetic set relations.	2005	teractive [java] applicati
15550481	java	CRAVE: a database, middleware and visualization system for phenotype ontologies.	2005	ccessible [java] applicati
15546938	c++	PermutMatrix: a graphical environment to arrange gene expression profiles in optimal linear order.	2005	ms-visual [C++], has a cl
15541170	r	Calibration and assessment of channel-specific biases in microarray data with extended dynamical range.	2004	-platform [R package] aroma, wh
15531616	perl	ESTminer: a suite of programs for gene and allele identification.	2005	ritten in [perl] and are f
15531613	mathlab	The SBW-MATLAB interface.	2005	ce allows [matlab] users to
15531604	java	A Java tool for dynamic web-based 3D visualization of anatomy and overlapping gene or protein expression patterns.	2005	a [java] tool for
15509605	r	Implementation of a gene expression index calculation method based on the PDNN model.	2005	atistical [language r].
15509599	java	MedKit: a helper toolkit for automatic mining of MEDLINE/PubMed citations.	2005	veloped a [java] package,
15488149	java	Caryoscope: an Open Source Java application for viewing microarray data in a genomic context.	2004	en source [java] applicati
15479716	java	Circular genome visualization and exploration using CGView.	2005	wer) is a [java] applicati
15477491	c++	GenomeMixer: a complex genetic cross simulator.	2004	entation, [C++] source, a
15466910	r	BagBoosting for tumor classification with gene expression data.	2004	ble as an [R package] under gnu
15458579	perl	GeneXplorer: an interactive web application for microarray data visualization and analysis.	2004	load from [CPAN] http://se
15458579	javascript	GeneXplorer: an interactive web application for microarray data visualization and analysis.	2004	html and [javascript] to displa
15454413	r	arrayMagic: two-colour cDNA microarray quality control and preprocessing.	2005	the [R package] arraymagi
15454409	python	Modelling cellular systems with PySCeS.	2005	the [python] simulator
15381628	r	Analysis of array CGH data: from signal ratio to gain and loss of DNA regions.	2004	the [R package] glad (gai
15377505	perl	HaploPainter: a tool for drawing pedigrees with complex haplotypes.	2005	ritten in [perl] and may b
15374874	c	Clann: investigating phylogenetic information through supertree analyses.	2005	en in the [C programming] language.
15374872	r	An experimental evaluation of a loop versus a reference design for two-channel microarrays.	2005	the data [and R] code are
15374871	r	VarMixt: efficient variance modelling for the differential analysis of replicated gene expression data.	2005	the [R package] is freely
15374867	mathlab	Improving genome annotations using phylogenetic profile anomaly detection.	2005	ted using [matlab] and open
15374864	java	ESTminer: a Web interface for mining EST contig and cluster databases.	2005	mented in [java] and the
15374860	mathlab	Reliability analysis of microarray data using fuzzy c-means and normal mixture modeling based classification methods.	2005	rms where [matlab] is availa
15374858	java	Expression-based monitoring of transcription factor activity: the TELiS database.	2005	erlocking [java] applicati
15355552	mathlab	Iterative class discovery and feature selection using Minimal Spanning Trees.	2004	ions. the [matlab] programs
15353451	mathlab	A Bayesian approach to reconstructing genetic regulatory networks with hidden factors.	2005	x.htm and [matlab] source co
15353448	java	SNAP: workbench management tool for evolutionary population genetic analysis.	2005	kbench, a [java] program t
15347576	perl	easyLINKAGE: a PERL script for easy and automated two-/multi-point linkage analyses.	2005	inkage: a [perl] script fo
15339346	c++	Estimating mutual information using B-spline functions--an improved similarity measure for analysing gene expression data.	2004	easures.a [C++] source co
15339345	r	Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE).	2004	ool or as [R language] scripts a
15333457	java	OntologyTraverser: an R package for GO analysis.	2005	stem uses [java] to instan
15333457	r	OntologyTraverser: an R package for GO analysis.	2005	erser: an [R package] for go an
15319258	java	Simulating genetic networks made easy: network construction with simple building blocks.	2005	the [java] program,
15310559	python	BlastAlign: a program that uses blast to align problematic nucleotide sequences.	2005	perl and [python] and will
15310559	perl	BlastAlign: a program that uses blast to align problematic nucleotide sequences.	2005	s of both [perl] and pytho
15308543	java	SNP Chart: an integrated platform for visualization and interpretation of microarray genotyping data.	2005	hart is a [java] applicati
15297302	java	Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprinting.	2004	her via a [java] user inte
15297301	r	Network structures and algorithms in Bioconductor.	2005	rithms in [Bioconductor].
15297299	perl	GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes.	2004	-oriented [perl] modules f
15297296	r	limmaGUI: a graphical user interface for linear modeling of microarray data.	2004	ted as an [R package]. the soft
15284097	java	CLANS: a Java application for visualizing protein families based on pairwise similarity.	2004	clans: a [java] applicati
15271780	mathlab	A probabilistic measure for alignment-free sequence comparison.	2004	ritten in [matlab] are avail
15271779	java	Data exploration tools for the Gene Ontology database.	2004	based on [java] 2 enterpr
15271778	mathlab	Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data.	2004	e a novel [matlab] toolbox f
15262800	c	An efficient algorithm for detecting frequent subgraphs in biological networks.	2004	ms in the [C programming] language
15262781	c++	Analysis of domain correlations in yeast protein complexes.	2004	the ncbi [C++] toolkit.
15262778	r	Statistical modeling of sequencing errors in SAGE libraries.	2004	ted as an [R package]. an onlin
15262777	mathlab	Deconvolving cell cycle expression data with complementary information.	2004	[matlab] implement
15256416	r	Importing MAGE-ML format microarray data into BioConductor.	2004	data into [Bioconductor].
15256415	r	A graph-theoretic approach to testing associations between disparate sources of functional genomics data.	2004	ttp://www.[Bioconductor].org.
15256401	perl	CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data.	2004	tem, csh, [perl] and mysql
15253776	java	Base-By-Base: single nucleotide-level analysis of whole viral genome alignments.	2004	net using [java] web start
15247095	java	VisRD--visual recombination detection.	2004	ritten in [java] and is de
15230973	perl	mlstdbNet - distributed multi-locus sequence typing (MLST) databases.	2004	rsed by a [perl] cgi scrip
15201188	java	The CRASSS plug-in for integrating annotation data with hierarchical clustering results.	2004	nted as a [java] plug-in f
15201186	java	SNPicker: a graphical tool for primer picking in designing mutagenic endonuclease restriction assays.	2004	mented in [java], which si
15201182	c++	Breakpoint identification and smoothing of array comparative genomic hybridization data.	2004	in visual [C++], has a us
15189572	mathlab	M-CGH: analysing microarray-based CGH experiments.	2004	-cgh is a [matlab] toolbox w
15180939	java	A statistical framework for the design of microarray experiments and effective detection of differential gene expression.	2004	nted as a [java] applicati
15180930	java	Java Treeview--extensible visualization of microarray data.	2004	[java] treeview-
15176974	perl	Detection of chromosomal regions showing differential gene expression in human skeletal muscle and in alveolar rhabdomyosarcoma.	2004	equently, [perl] software
15166027	r	Regulatory motif finding by logic regression.	2004	d.html an [R package] for mfure
15145813	java	ClutrFree: cluster tree visualization and interpretation.	2004	clutrfree [java] source co
15117754	mathlab	Identification of DNA regulatory motifs using Bayesian variable selection.	2004	the [matlab] code for
15117748	java	YAdumper: extracting and translating large information volumes from relational databases to structured flat files.	2004	mper is a [java] applicati
15113410	java	A web services choreography scenario for interoperating bioinformatics applications.	2004	ard coded [java] applicati
15105279	java	GDPC: connecting researchers with multiple integrated data sources.	2004	ritten in [java] and provi
15105278	java	ProteoMix: an integrated and flexible system for interactively analyzing large numbers of protein sequences.	2004	suite of [java] programs
15087316	java	Sfixem--graphical sequence feature display in Java.	2004	isplay in [java].
15087313	mathlab	Analysis of longitudinal metabolomics data.	2004	files for [matlab] for the a
15087311	fortran	MathSBML: a package for manipulating SBML-based biological models.	2004	html and [fortran]. by acces
15073026	java	ArrayNorm: comprehensive normalization and analysis of microarray data.	2004	dependent [java] applicati
15073025	java	Pedro: a configurable data entry tool for XML.	2004	edro is a [java] applicati
15073017	perl	Alignment of RNA base pairing probability matrices.	2004	mented in [perl] and can b
15072998	java	Web-based kinetic modelling using JWS Online.	2004	ser based [java] applets,
15059840	java	MuSiC: a tool for multiple sequence alignment with constraints.	2004	mented in [java] language
15059837	mathlab	Extraction of fluorescent cell puncta by adaptive fuzzy segmentation.	2004	ritten in [matlab] are avail
15059834	java	Designing and executing scientific workflows with a programmable integrator.	2004	irements: [java] v1.3 (htt
15059827	perl	SCANMS: adjusting for multiple comparisons in sliding window neutrality tests.	2004	a [perl] utility c
15059823	c++	PedSplit: pedigree management for stratified analysis.	2004	cutables, [C++] source co
15059819	java	Pelican: pedigree editor for linkage computer analysis.	2004	igher). a [java] web start
15044243	mathlab	Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle.	2004	[matlab] code and
15044236	java	ConSSeq: a web-based application for analysis of amino acid conservation based on HSSP database and within context of structure.	2004	nted as a [java] applet.
15040818	perl	The tissue microarray data exchange specification: implementation by the Cooperative Prostate Cancer Tissue Resource.	2004	formative [perl] script. t
15033875	r	Degrees of differential gene expression: detecting biologically significant expression differences and estimating their magnitudes.	2004	rg or www.[Bioconductor].org
15033871	perl	Optimization models for cancer classification: extracting gene interaction information from microarray expression data.	2004	do.com. a [perl] script th
15033870	java	Phylo-VISTA: interactive visualization of multiple DNA sequence alignments.	2004	wser with [java] plug-in 1
15033868	r	Enhancing scatterplots with smoothed densities.	2004	or matlab [and R] are avail
15033868	mathlab	Enhancing scatterplots with smoothed densities.	2004	tions for [matlab] and r are
14988125	mathlab	Decoupling dynamical systems for pathway identification from metabolic profiles.	2004	with the [matlab] module bs
14988124	r	Mixture models for assessing differential expression in complex tissues using microarray data.	2004	ds in the [R language] can be do
14988123	java	GeneCluster 2.0: an advanced toolset for bioarray analysis.	2004	and-alone [java] applicati
14988118	r	matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements.	2004	the [R package] matchprob
14988110	mathlab	Robust PCA and classification in biosciences.	2004	rt of the [matlab] toolbox f
14988107	java	TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments.	2004	is a new [java] graphical
14988100	java	Haplotypes histories as pathways of recombinations.	2004	oped on a [java] platform
14962941	java	ToPNet--an application for interactive analysis of expression data and biological networks.	2004	is a pure [java] applicati
14962938	mathlab	Modeling T-cell activation using gene expression profiling and state-space models.	2004	data and [matlab] computer
14962926	c++	A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences.	2004	mented in [C++] in a prog
14962918	python	Amplicon: software for designing PCR primers on aligned DNA sequences.	2004	form with [python] 2.3 insta
14962913	perl	Simple sequence repeat marker loci discovery using SSR primer.	2004	ritten in [perl] and is fr
14960475	perl	VisCoSe: visualization and comparison of consensus sequences.	2004	mand line [perl] script fo
14960472	java	The Jalview Java alignment editor.	2004	e jalview [java] alignment
14960468	c++	LDDist: a Perl module for calculating LogDet pair-wise distances for protein and nucleotide sequences.	2004	mented in [C++] that allo
14960468	perl	LDDist: a Perl module for calculating LogDet pair-wise distances for protein and nucleotide sequences.	2004	lddist: a [perl] module fo
14960456	r	affy--analysis of Affymetrix GeneChip data at the probe level.	2004	age is an [R package] of functi
14871871	c++	Bayesian mixture model based clustering of replicated microarray data.	2004	esponding [C++] code are
14871861	python	Open source clustering software.	2004	nerated a [python] and a per
14871861	c++	Open source clustering software.	2004	her c and [C++] programs.
14871861	perl	Open source clustering software.	2004	hon and a [perl] interface
14871859	java	CNplot: visualizing pre-clustered networks.	2004	a [java] implement
14764576	java	Ontologizing gene-expression microarray data: characterizing clusters with Gene Ontology.	2004	xml-based [java] applicati
14764570	java	GelScape: a web-based server for interactively annotating, manipulating, comparing and archiving 1D and 2D gel images.	2004	. it uses [java] applet-se
14764568	perl	Sequence analysis and membrane partitioning energies of alpha-helical antimicrobial peptides.	2004	zed using [perl] programs.
14764558	java	An evaluation of new criteria for CpG islands in the human genome as gene markers.	2004	cpgie, a [java] software
14764554	c	Multiple sequence alignment in parallel on a workstation cluster.	2004	kstations [using C] and messa
14764551	r	ChromoViz: multimodal visualization of gene expression data onto chromosomes using scalable vector graphics.	2004	viz is an [R package] for the v
14751995	perl	Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments.	2004	atlab and [perl] code used
14751995	mathlab	Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments.	2004	the [matlab] and perl
14751994	mathlab	Predicting protein structure classes from function predictions.	2004	[matlab] code is a
14751988	java	Java-based application framework for visualization of gene regulatory region annotations.	2004	es, using [java] technolog
14751975	java	Visualization of near-optimal sequence alignments.	2004	sent to a [java] applet, w
14751975	c++	Visualization of near-optimal sequence alignments.	2004	face to a [C++] program g
14734327	r	APE: Analyses of Phylogenetics and Evolution in R language.	2004	official [R package] archive a
14734323	java	JDotter: a Java interface to multiple dotplots generated by dotter.	2004	dotter: a [java] interface
14734312	mathlab	Comparative evaluation of word composition distances for the recognition of SCOP relationships.	2004	all [matlab] code used
14734308	python	A comparative phylogenetic approach for dating whole genome duplication events.	2004	en in the [python] programmi
14734306	perl	Computational identification of novel chitinase-like proteins in the Drosophila melanogaster genome.	2004	[perl] program a
14734305	perl	Transposable element annotation of the rice genome.	2004	a set of [perl] scripts.
14715091	perl	Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures.	2004	in c and [perl]. the code
14706121	python	PyEvolve: a toolkit for statistical modelling of molecular evolution.	2004	standard [python] code to d
14693822	java	BugView: a browser for comparing genomes.	2004	view is a [java] applicati
14693819	c++	GRIL: genome rearrangement and inversion locator.	2004	mented in [C++] and runs
14693816	mathlab	Adjustment of systematic microarray data biases.	2004	[matlab] software
14693814	r	A global test for groups of genes: testing association with a clinical outcome.	2004	ttp://www.[Bioconductor].org
14693813	java	VizStruct: exploratory visualization for gene expression profiling.	2004	ritten in [java] and matla
14693813	mathlab	VizStruct: exploratory visualization for gene expression profiling.	2004	java and [matlab] and softw
14693803	r	Identifying periodically expressed transcripts in microarray time series data.	2004	ed in the [R package] genets av
14678565	java	AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis.	2003	ddleware, [java], jdbc, an
14668247	perl	Characterizing gene sets with FuncAssociate.	2003	code (in [perl] and c) is
14668233	r	A CART-based approach to discover emerging patterns in microarray data.	2003	atistical [language r] implement
14668224	java	caCORE: a common infrastructure for cancer informatics.	2003	provides [java], simple o
14668219	c	Efficient estimation of emission probabilities in profile hidden Markov models.	2003	lgorithms [written in C] language
14668218	java	JXP4BIGI: a generalized, Java XML-based approach for biological information gathering and integration.	2003	eralized, [java] xml-based
14630669	c++	NCL: a C++ class library for interpreting data files in NEXUS format.	2003	ncl: a [C++] class lib
14630667	c++	Libsequence: a C++ class library for evolutionary genetic analysis.	2003	quence: a [C++] class lib
14630665	mathlab	Gene Expression Dynamics Inspector (GEDI): for integrative analysis of expression profiles.	2003	ritten in [matlab], and bina
14630660	python	PDB file parser and structure class implemented in Python.	2003	mented in [python].
14630649	mathlab	MGraph: graphical models for microarray data analysis.	2003	roduces a [matlab] toolbox,
14604444	java	PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis.	2003	ritten in [java] that can
14594724	java	RED-T: utilizing the Ratios of Evolutionary Distances for determination of alternative phylogenetic events.	2003	ed-t is a [java] applicati
14594722	java	LDA--a java-based linkage disequilibrium analyzer.	2003	user, the [jre] version 1
14594719	java	An unsupervised hierarchical dynamic self-organizing approach to cancer class discovery and marker gene identification in microarray data.	2003	[java] software
14594459	java	GeneViTo: visualizing gene-product functional and structural features in genomic datasets.	2003	propriate [java] runtime e
14583100	java	A knowledge discovery object model API for Java.	2003	l api for [java].
14555636	java	GCHap: fast MLEs for haplotype frequencies by gene counting.	2003	the [java] classes a
14555628	r	Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays.	2003	th s-plus [and R] functions
14534191	python	Finding optimal degenerate patterns in DNA sequences.	2003	the [python] script su
14512356	java	The design of Jemboss: a graphical user interface to EMBOSS.	2003	ritten in [java] and is do
14512356	c	The design of Jemboss: a graphical user interface to EMBOSS.	2003	en in the [C language]. another
14512353	c	Transformation and normalization of oligonucleotide microarray data.	2003	a program [written in C] is availa
14512352	java	Controlling false-negative errors in microarray differential expression analysis: a PRIM approach.	2003	estanding [java] applicati
12962546	perl	Genome-wide prediction, display and refinement of binding sites with information theory-based models.	2003	cripts in [perl]. multi-pr
12875658	java	Evolutionary algorithms for the selection of single nucleotide polymorphisms.	2003	spea2) in [java]. our impl
12874048	mathlab	Exact significance levels for the maximum chi(2) method of detecting recombination.	2003	[matlab] source co
12874047	mathlab	Estimation of transformation parameters for microarray data.	2003	r and [matlab] code and
12835278	c	Calculation of helix packing angles in protein structures.	2003	[C language] source co
12835277	perl	GeneComber: combining outputs of gene prediction programs for improved results.	2003	en in the [perl] programmi
12835276	java	Longest biased interval and longest non-negative sum interval.	2003	[java] code of t
12835275	java	TableView: portable genomic data visualization.	2003	ritten in [java], tablevie
12801871	mathlab	Novel clustering algorithm for microarray expression data in a truncated SVD space.	2003	ilable as [matlab] programs
12801870	r	Simultaneous gene clustering and subset selection for sample classification via MDL.	2003	ed in the [R language]. the sour
12801869	r	Bagging to improve the accuracy of a clustering procedure.	2003	ttp://www.[Bioconductor].org.
12801867	c++	K-ary clustering with optimal leaf ordering for gene expression data.	2003	rithms in [C++] on the li
12761071	java	Ligand-Info, searching for similar small compounds using index profiles.	2003	uires the [java] runtime e
12761070	java	ACGT-a comparative genomics tool.	2003	ritten in [java] and can b
12761060	mathlab	Fuzzy C-means method for clustering microarray data.	2003	text and [matlab] functions
12761052	java	FPV: fast protein visualization using Java 3D.	2003	ion using [java] 3d.
12724301	perl	GeneMerge--post-genomic analysis, data mining, and hypothesis testing.	2003	ritten in [perl] that retu
12724295	java	ALES: cell lineage analysis and mapping of developmental events.	2003	compliant [java] 2 environ
12720549	c++	DNA microarray data and contextual analysis of correlation graphs.	2003	e data. a [C++] implement
12697067	perl	Significance analysis of lexical bias in microarray data.	2003	ilable as [perl] source or
12691998	java	GoFish finds genes with combinations of Gene Ontology attributes.	2003	fish is a [java] applicati
12691997	java	Java editor for biological pathways.	2003	[java] editor fo
12691990	java	Client-server environment for high-performance gene expression data analysis.	2003	scalable [java] environme
12651733	java	PedNavigator: a pedigree drawing servlet for large and inbred populations.	2003	ritten in [java] and is in
12651728	mathlab	MatArray: a Matlab toolbox for microarray data.	2003	tarray: a [matlab] toolbox f
12611807	mathlab	Alignment-free sequence comparison-a review.	2003	mented in [matlab] code and
12611802	mathlab	Clustering of time-course gene expression data using a mixed-effects model with B-splines.	2003	[matlab] programs
12611799	mathlab	An information theoretic approach for analyzing temporal patterns of gene expression.	2003	nsi c and [matlab] (mathwork
12611798	fortran	Can transcriptome size be estimated from SAGE catalogs?	2003	to share [fortran] sourcecod
12584141	perl	Wrapping up BLAST and other applications for use on Unix clusters.	2003	eloped in [perl] on a 20-n
12584131	perl	Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP.	2003	ritten in [perl] and is fr
12538267	python	ARIA: automated NOE assignment and NMR structure calculation.	2003	sspeaks), [python] scripts f
12538266	c	DPX: for the analysis of the protein core.	2003	e program [written in C] and its s
12538262	perl	G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining.	2003	a set of [perl] libraries
12538259	c	RnaViz 2: an improved representation of RNA secondary structure.	2003	ng pieces [written in C] and in th
12538256	java	AVA: visual analysis of gene expression microarray data.	2003	zer) is a [java] program t
12538252	c++	An efficient algorithm for minimal primer set selection.	2003	mented in [C++] programmi
12538248	mathlab	FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps.	2003	ckage for [matlab] and facil
12538244	perl	A naive Bayes model to predict coupling between seven transmembrane domain receptors and G-proteins.	2003	t for the [perl] program f
12538241	python	Rank order metrics for quantifying the association of sequence features with gene regulation.	2003	a [python] program f
12538238	r	A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.	2003	rt of the [R package] affy, whi
12538236	mathlab	Chemometric modelling based on 2D-fluorescence spectra without a calibration measurement.	2003	the [mathlab] routine i
12513700	java	SeqVISTA: a graphical tool for sequence feature visualization and comparison.	2003	em with a [java] 1.4 virtu
12511063	python	Phase4: automatic evaluation of database search methods.	2002	language [python] whose obj
12499313	javascript	ModView, visualization of multiple protein sequences and structures.	2003	d through [javascript] commands
12499308	r	An extensible application for assembling annotation for genomic data.	2003	der is an [R package] for assem
12499304	c++	Simulating complex traits influenced by genes with fuzzy-valued effects in pedigreed populations.	2003	a [C++] library f
12493080	java	ORFer--retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files.	2002	a [java] program w
12424130	java	Poxvirus Orthologous Clusters (POCs).	2002	ocs) is a [java] client-se
12424129	perl	GeneCards 2002: towards a complete, object-oriented, human gene compendium.	2002	-oriented [perl], migratio
12401134	c++	SeqHound: biological sequence and structure database as a platform for bioinformatics research.	2002	erl, c or [C++] remote ap
12401134	perl	SeqHound: biological sequence and structure database as a platform for bioinformatics research.	2002	through a [perl], c or c++
12398795	perl	Making sense of EST sequences by CLOBBing them.	2002	ed on the [perl] scripting
12385980	c++	Modeling splicing sites with pairwise correlations.	2002	the [C++] source co
12376386	perl	Genquire: genome annotation browser/editor.	2002	existing [bioperl] data mode
12376379	c++	Threading using neural nEtwork (TUNE): the measure of protein sequence-structure compatibility.	2002	the [C++] source co
12376376	mathlab	Gene perturbation and intervention in probabilistic Boolean networks.	2002	ritten in [matlab] for simul
12366869	perl	Oliz, a suite of Perl scripts that assist in the design of microarrays using 50mer oligonucleotides from the 3' untranslated region.	2002	suite of [perl] scripts t
12230038	java	The Bio* toolkits--a brief overview.	2002	ython and [biojava] projects
12230038	python	The Bio* toolkits--a brief overview.	2002	bioperl, [biopython] and bioja
12230038	perl	The Bio* toolkits--a brief overview.	2002	en source [bioperl], biopytho
12217927	java	An ontology driven architecture for derived representations of macromolecular structure.	2002	ader. the [java] source co
12217926	java	Applications of Tree-Maps to hierarchical biological data.	2002	[java] class fil
12217919	java	VIZARD: analysis of Affymetrix Arabidopsis GeneChip data.	2002	zard is a [java] program c
12176842	perl	DiffTool: building, visualizing and querying protein clusters.	2002	. all the [perl] sources a
12176840	mathlab	MArray: analysing single, replicated or reversed microarray experiments.	2002	rray is a [matlab] toolbox w
12176838	perl	TFBS: Computational framework for transcription factor binding site analysis.	2002	-oriented [perl] modules f
12169562	java	PseudoViewer: automatic visualization of RNA pseudoknots.	2002	nted in a [java] program,
12117796	c	CX, an algorithm that identifies protruding atoms in proteins.	2002	e program [written in C] and its s
12075029	java	BAOBAB: a Java editor for large phylogenetic trees.	2002	baobab: a [java] editor fo
12050079	perl	A bioinformatics tool to select sequences for microarray studies of mouse models of oncogenesis.	2002	ent (dbi) [perl] to annota
12050073	java	Gene structure identification with MyGV using cDNA evidence and protein homologs to improve ab initio predictions.	2002	ritten in [java] and is fr
12028595	java	RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs.	2002	ral c and [java] programs.
12028595	perl	RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs.	2002	mented as [perl] pipeline
12019022	perl	NBLAST: a cluster variant of BLAST for NxN comparisons.	2002	c/c++ and [perl] applicati
12016048	java	Compensation for nucleotide bias in a genome by representation as a discrete channel with noise.	2002	ignal.' a [java] applicati
11934743	java	PatternHunter: faster and more sensitive homology search.	2002	t support [java]. patternh
11847095	javascript	The EBI SRS server--recent developments.	2002	icksearch [javascript] interface
11836236	java	PCSB--a program collection for structural biology and biophysical chemistry.	2002	ackage of [java] classes s
11836235	java	Genesis: cluster analysis of microarray data.	2002	sy to use [java] suite for
11836221	java	The Binding Database: data management and interface design.	2002	cted with [java] servlet t
11836216	java	Automated ortholog inference from phylogenetic trees and calculation of orthology reliability.	2002	mented in [java] and calcu
11751242	c	CONSEL: for assessing the confidence of phylogenetic tree selection.	2001	grams are [written in C] language.
11751232	perl	MELTING, computing the melting temperature of nucleic acid duplex.	2001	n-source. [perl] scripts a
11751230	c	A neural network classifier capable of recognizing the patterns of all major subcellular structures in fluorescence microscope images of HeLa cells.	2001	functions [written in C]. the scri
11751230	mathlab	A neural network classifier capable of recognizing the patterns of all major subcellular structures in fluorescence microscope images of HeLa cells.	2001	products [matlab], s-plus,
11751227	perl	How to reconstruct a large genetic network from n gene perturbations in fewer than n(2) easy steps.	2001	a [perl] implement
11724739	perl	Database-driven multi locus sequence typing (MLST) of bacterial pathogens.	2001	a set of [perl] scripts f
11707150	java	FastGroup: a program to dereplicate libraries of 16S rDNA sequences.	2001	tgroup, a [java] program d
11673244	mathlab	Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome.	2001	[matlab] (mathwork
11591214	java	FOUNTAIN: a JAVA open-source package to assist large sequencing projects.	2001	untain: a [java] open-sour
11590102	perl	GeneMachine: gene prediction and sequence annotation.	2001	suite of [perl] programs
11524384	python	SIR: a simple indexing and retrieval system for biological flat file databases.	2001	ritten in [python]. since th
11524378	c++	Multi-query sequence BLAST output examination with MuSeqBox.	2001	standard [C++] and is fr
11524374	c++	The Bioinformatics Template Library--generic components for biocomputing.	2001	ndard for [C++] includes
11448890	java	A Java applet for visualizing protein-protein interaction.	2001	a [java] applet fo
11448888	java	PAL: an object-oriented programming library for molecular evolution and phylogenetics.	2001	ection of [java] classes f
11448887	c	ADAPTSITE: detecting natural selection at single amino acid sites.	2001	urce code [written in C], binary f
11331235	perl	Retrieval and on-the-fly alignment of sequence fragments from the HIV database.	2001	ection of [perl] scripts t
11301314	java	ATV: display and manipulation of annotated phylogenetic trees.	2001	atv) is a [java] tool for
11301307	java	J-Express: exploring gene expression data using Java.	2001	ata using [java].
11301303	java	NIFAS: visual analysis of domain evolution in proteins.	2001	a [java] applet, n
11238077	perl	Virtual PCR.	2001	[perl] code and
11159329	perl	Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology.	2000	ped using [perl] and perl/
11159311	perl	Arbor 3D: an interactive environment for examining phylogenetic and taxonomic trees in multiple dimensions.	2000	irix 6.4, [perl] parsers,
11120685	java	Artemis: sequence visualization and annotation.	2000	mented in [java], and can
11108704	c++	BALL--rapid software prototyping in computational molecular biology. Biochemicals Algorithms Library.	2000	mework in [C++] that has
11038333	python	Object-oriented parsing of biological databases with Python.	2000	ases with [python].
10871272	java	Viral Genome DataBase: storing and analyzing genes and proteins from complete viral genomes.	2000	-friendly [java] gui. resu
10869040	java	A browser for expression data.	2000	xtensible [java] applicati
10869029	java	JESAM: CORBA software components to create and publish EST alignments and clusters.	2000	y example [java] applet br
10869029	c++	JESAM: CORBA software components to create and publish EST alignments and clusters.	2000	ll the c, [C++] and idl c
10869028	perl	GABAagent: a system for integrating data on GABA receptors.	2000	ritten in [perl] script, a
10869022	java	Storing biological sequence databases in relational form.	2000	perl and [java] in combin
10869022	perl	Storing biological sequence databases in relational form.	2000	ons using [perl] and java
10869012	c	Homology-based gene structure prediction: simplified matching algorithm using a translated codon (tron) and improved accuracy by allowing for long gaps.	2000	ritten in [ansi-C] and the t
10745985	java	IMAGEne I: clustering and ranking of I.M.A.G.E. cDNA clones corresponding to known genes.	1999	intuitive [java] interface
10743559	fortran	A simple algorithm for detecting circular permutations in proteins.	1999	a [fortran] program t
10743555	perl	Evaluation of gene prediction software using a genomic data set: application to Arabidopsis thaliana sequences.	1999	set, the [perl] programs
10705440	perl	MULTICLUSTAL: a systematic method for surveying Clustal W alignment parameters.	1999	stal is a [perl] script de
10705437	java	ORBIT: an integrated environment for user-customized bioinformatics tools.	1999	upporting [java]. the syst
10705434	r	An analysis of the Protein Data Bank in search of temporal and global trends.	1999	esolution [and R] value sho
10498781	perl	Swissknife - 'lazy parsing' of SWISS-PROT entries.	1999	a set of [perl] modules w
10487877	java	Interactive data input into the GeneNet database.	null	base, the [java] graphical
10366663	java	JaDis: computing distances between nucleic acid sequences.	1999	adis is a [java] applicati
10366658	java	CRAWview: for viewing splicing variation, gene families, and polymorphism in clusters of ESTs and full-length sequences.	1999	awview, a [java] based vis
10320405	java	CoPE: a collaborative pedigree drawing environment.	1999	ncludes a [java] program f
10320399	java	DINAMO: interactive protein alignment and model building.	1999	web-based [java] applet at
10068695	c++	Genetic Simulation Library.	1999	a set of [C++] programs
9918957	java	WEBMAP: radiation hybrid mapping on the WWW.	1998	a [java] interface
9918956	perl	SPEM: a parser for EMBL style flat file database entries.	1998	a set of [perl] modules f
9918950	java	Representing metabolic pathway information: an object-oriented approach.	1998	ped using [java], an objec
9789101	java	A web server to locate periodicities in a sequence	1998	er with a [java] interface
9789101	c++	A web server to locate periodicities in a sequence	1998	ritten in [C++], which im
9789100	java	A visual environment for the manipulation and integration of JAVA beans.	1998	ration of [java] beans.
9789091	perl	GeneCards: a novel functional genomics compendium with automated data mining and query reformulation support.	1998	mpiled by [perl] scripts t
9730921	perl	The LabBase system for data management in large scale biology research laboratories.	1998	ritten in [perl].
9694997	java	Graphical interface to the genetic network database GeNet.	1998	esigned a [java] applet wh
9694992	java	GeneNet: a gene network database and its automated visualization.	1998	ritten in [java] provides
9694986	java	The bio-objects project. Part I: the object data model core elements.	1998	aries and [java] binary fi
9694986	c++	The bio-objects project. Part I: the object data model core elements.	1998	assemble [C++] libraries
9694985	c++	Formal design and implementation of an improved DDBJ DNA database with a new schema and object-oriented library.	1998	nted as a [C++] object-or
9682060	c	CloneIt: finding cloning strategies, in-frame deletions and frameshifts.	1998	ritten in [ansi-C] language,
9682055	perl	Removing near-neighbour redundancy from large protein sequence collections.	1998	90, and a [perl] script (n
9520496	perl	The Merck Gene Index browser: an extensible data integration system for gene finding, gene characterization and EST data mining.	1998	suite of [perl] routines.
9183530	c++	Object-oriented developmental environment for image-analysis applications: implementation for 2D gel electrophoretogram analysis.	1997	lities of [C++] programmi
9146965	perl	Hopper: software for automating data tracking and flow in DNA sequencing.	1997	a central [perl] program,
8872394	fortran	IBIS version 3: an OSF/Motif-based interface for IBIS--integrated biological imaging system.	1996	ritten in [fortran] 77 for co
8744774	c++	Object-oriented sequence analysis: SCL--a C++ class library.	1996	s: scl--a [C++] class lib
8590181	c	MATRIX SEARCH 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of weight matrices.	1995	is in the ['C'] language,
8590180	c	Compression of protein sequence databases.	1995	interface [written in C] which all
8590169	fortran	A FORTRAN program to simulate the evolution of genetic variability in a small population.	1995	a [fortran] program t
8521055	c	DNASTAT: a Pascal unit for the statistical analysis of DNA and protein sequences.	1995	ritten in [ansi-C] for pcs a
7796269	fortran	Simulating efficiently the evolution of DNA sequences.	1995	nu-driven [fortran] programs
7704656	c++	Design and application of PDBlib, a C++ macromolecular class library.	1994	pdblib, a [C++] macromole
7828069	fortran	A consensus procedure for predicting the location of alpha-helical transmembrane segments in proteins.	1994	ethods. a [fortran] program h
7528631	c	Nucleic acid modeling tool (NAMOT): an interactive graphic tool for modeling nucleic acid structures.	1994	rogram is [written in C] using xvi
8019868	c++	MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers.	1994	ritten in [C++] and is in
8143154	c	FT3D: three-dimensional Fourier analysis on small Unix workstations for electron microscopy and tomographic studies.	1993	en in the [C language] for unix
8293331	c	A general UNIX interface for biocomputing and network information retrieval software.	1993	ogram was [written in C] language
7507400	c	Automatic display of RNA secondary structures.	1993	programs [written in C] language
8402211	c	SCAMP: a general-purpose simulator and metabolic control analysis program.	1993	rogram is [written in C] and is po
8481826	c	A hypertext-like approach to navigating through the GCG sequence analysis package.	1993	en in the [C language] and using
1468016	fortran	IBIS integrated biological imaging system: electron micrograph image-processing software running on Unix workstations.	1992	ritten in [fortran] 77 and ru
1422877	c++	METASIM: object-oriented modelling of cell regulation.	1992	itions in [C++] is presen
1633564	c++	Redesigning, implementing and integrating Escherichia coli genome software tools with an object-oriented database system.	1992	rted into [C++], and then
1353007	fortran	A microcomputer FORTRAN program for rapid determination of lethal concentrations of biocides in mosquito control.	1992	ocomputer [fortran] program f
1591615	c	CLUSTAL V: improved software for multiple sequence alignment.	1992	which is [written in C] and can b
1568123	fortran	MULTICOMP: a program package for multiple sequence comparison.	1992	mented in [fortran] 77 for va
2059852	fortran	PROMOT: a FORTRAN program to scan protein sequences against a library of known motifs.	1991	promot: a [fortran] program t
2059843	fortran	Software for the development and evaluation of probabilistic identification matrices.	1991	ritten in [fortran] 77 and ca
2207751	c	POLCA, a library running in a modern environment, implements a protocol for averaging randomly oriented images.	1990	polca is [written in C] and runs
2207747	c	MUCIDS: an operative C environment for acquisition and processing of polarized-light scattered from biological specimens.	1990	tware was [written in C] lattice a
2207743	c	A C version of Fourier-derived affinity spectrum analysis (FASA) to resolve binding heterogeneity.	1990	re in the [language C]. new appl
2207743	fortran	A C version of Fourier-derived affinity spectrum analysis (FASA) to resolve binding heterogeneity.	1990	ritten in [fortran], is exten
2207741	fortran	The development of a high-order Taylor expansion solution to the chemical rate equation for the simulation of complex biochemical systems.	1990	develop a [fortran] algorithm
2361183	c	Olga--oligonucleotide primer design program for the Atari ST.	1990	standard ['C'] and makes
2310954	fortran	Analysis of mixed lipid extracts using 1H NMR spectra.	1990	ts. a new [fortran] algorithm
2819513	fortran	HYLAS: program for generating H curves (abstract three-dimensional representations of long DNA sequences).	1989	ritten in [fortran] with sepa
2766006	fortran	A FORTRAN subroutine to compute inbreeding and kinship coefficients according to the number of ancestral generations.	1989	a [fortran] subroutin
2924171	fortran	SDSE: a software package to simulate the evolution of a pair of DNA sequences.	1989	eme. five [fortran] programs,
3208177	fortran	A program for drawing evolutionary trees.	1988	ritten in [fortran] 66, which
3167604	fortran	Computer program Jamsek combining statistical and stereochemical rules for the prediction of protein secondary structure.	1988	ritten in [fortran] for an ic
3167596	fortran	A computer program to display codon changes caused by mutagenesis.	1988	a [fortran] program f
3453239	fortran	A computer program for the design of optimal synthetic oligonucleotide probes for protein coding genes.	1987	ritten in [fortran] 77 to loc
3453234	fortran	Interfacing similarity search software with the sequence retrieval system ACNUC.	1987	ritten in [fortran] 77 and is
3453230	fortran	A modified Chou and Fasman protein structure algorithm.	1987	a [fortran] program p
3453213	fortran	Programs for evaluating and characterising bacterial taxonomic data.	1987	ritten in [fortran] 77 and im
3453210	c	Pattern matching of biological sequences with limited storage.	1987	mented in [C programming] language
3450370	fortran	Visualization of the entire surface of a protein by cartographic projection.	1986	ritten in [fortran] iv (surfa
3450368	fortran	An improved FORTRAN 77 recombinant DNA database management system with graphic extensions in GKS.	1986	improved [fortran] 77 recomb
3880341	fortran	ACNUC--a portable retrieval system for nucleic acid sequence databases: logical and physical designs and usage.	1985	ritten in [fortran] 77 which
3880336	fortran	Assessing the biological significance of primary structure consensus patterns using sequence databanks. I. Heat-shock and glucocorticoid control elements in eukaryotic promoters.	1985	describe [fortran] 77 softwa

	.PHONY:all
	JVARKIT_HOME?=${HOME}/src/jvarkit-git/dist

	all: graph.png

	graph.png : biostar251002.tsv script.gnuplot
	grep -v YEAR $< \| awk -F ' ' '{printf("%s\t%s\n", $4,$ 2);}'\| tr " " "_" \| grep -v null \|\
	sed 's/$$/ 1/'\| ${HOME}/src/cmd-utils/src/yxv2table -a sum -n 0 \| sed 's/^#/YEAR/' > graph.tsv && \
	gnuplot script.gnuplot
	rm -f graph.tsv

	biostar251002.tsv :
	echo -e "PMID\tLANG\tTITLE\tYEAR\tCONTEXT" > $@
	java -jar $(JVARKIT_HOME)/pubmeddump.jar 'Cabios[journal] OR Bioinformatics[journal]' \|\
	java -jar $(JVARKIT_HOME)/pubmedcodinglang.jar -c 2> /dev/null \|tr '"' ' ' \| tr '"' ' ' \|\
	tee /dev/tty >> $@

	set terminal svg size 1000,800;
	set output "graph.svg"
	set title "Bioinformatics/language"
	set key invert reverse Left outside
	set key autotitle columnheader
	set yrange [0:]
	set auto x
	set datafile separator "\t"
	unset xtics
	set xlabel "Year"
	set ylabel "Count"
	set xtics nomirror rotate by -45 scale 0
	set style data histogram
	set style histogram rowstacked
	set style fill solid border -1
	set boxwidth 0.75
	N=`awk 'NR==1 {print NF}' graph.tsv`
	plot 'graph.tsv' using 2:xtic(1), for [i=3:N] '' using i;

	cp "${HOME}/.mozilla/firefox/xxxxxxxxxxx.default/cookies.sqlite" tmp.sqlite

	# see https://gist.github.com/spk/5014421
	sqlite3 -header -separator ' ' tmp.sqlite "select host, case substr(host,1,1)='.' when 0 then 'FALSE' else 'TRUE' end, path, case isSecure when 0 then 'FALSE' else 'TRUE' end, expiry, name, value from moz_cookies;" > tmp.cookies


	seq 1 10 \| while read PAGE
	do

	curl -s --cookie tmp.cookies "https://api.github.com/search/repositories?q=bioinformatics&sort=stars&order=desc&page=${PAGE}" > tmp.json
	echo "var doc= JSON.parse(readFully('tmp.json'));for(var i in doc.items) {var project=doc.items[i]; print( project.name+'\t'+project.language+'\t'+project.description);} " \| jjs -scripting

	done \| sort \| uniq \| cut -f 2 \| sort \| uniq -c \| sort -n

	rm tmp.sqlite tmp.cookies

	1 FORTRAN
	1 OCaml
	1 Parrot
	1 TeX
	2 Clojure
	2 Julia
	2 Makefile
	2 Perl
	3 Go
	3 null
	3 Scala
	4 Groovy
	5 Java
	5 Jupyter Notebook
	5 Shell
	6 JavaScript
	7 C
	7 Ruby
	8 HTML
	10 R
	13 C++
	28 Python