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736 results • Page 2 of 15
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21
votes
14
replies
9.5k
views
Tool: trackplot: Fast and minimal dependency standalone R script to generate IGV style locus tracks from bigWig files
visualization igv ChIP-Seq R bigwigs
updated 11 months ago by 43k • written 3.5 years ago by ★ 3.2k
13
votes
14
replies
6.2k
views
9 follow
Tool: open-cravat: variant annotation tool
open-cravat
updated 11 months ago by 43k • written 5.4 years ago by ▴ 260
0
votes
13
replies
2.6k
views
Tool: HIT'nDRIVE: Network based cancer driver genes prioritization algorithm using Hitting Time
network driver-gene software
updated 10 months ago by 43k • written 6.8 years ago by ★ 1.1k
27
votes
13
replies
6.0k
views
Tool: DEA.R: Command line script for differential expression analysis with R packages (DESeq2/edgeR/limma-voom)
edgeR DESeq2 limma RNA-Seq
updated 10 months ago by 43k • written 7.8 years ago by 47k
53
votes
13
replies
5.7k
views
6 follow
Tool: I made a DNA/gene/bioinformatics-y workshop for 11-16 year olds which people may find useful
school-outreach
updated 16 months ago by 43k • written 9.0 years ago by ★ 4.0k
54
votes
13
replies
10k
views
6 follow
Tool: Bedtools: Analyzing Genomic Features
bedtools
updated 10 months ago by 43k • written 12.1 years ago by 100k
4
votes
13
replies
2.8k
views
Tool: SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
pathway-analysis visualization Pathview SBGN
updated 11 months ago by 43k • written 3.2 years ago by ▴ 430
11
votes
12
replies
4.9k
views
Tool: Mapsembler2 targeted micro assembly and visualization of the local assembly graph
minia mapsembler next-gen Assembly
updated 2.1 years ago by 43k • written 9.8 years ago by ▴ 900
27
votes
12
replies
11k
views
Tool: Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads.
QC Trimming Read Trimmer
updated 2.6 years ago by 43k • written 9.9 years ago by 20k
9
votes
12
replies
4.6k
views
Tool: fastp v0.9 released: an all-in-one FASTQ preprocessor (QC, adapters, trimming, quality filtering / cutting, splitting output ... )
fastq fastp open-source
updated 10 months ago by 43k • written 6.6 years ago by ★ 2.5k
10
votes
12
replies
1.9k
views
Tool: PanDepth, an ultra-fast and efficient genomic tool for coverage calculation
bam paf depth cram coverage
3 months ago by Huiyang ▴ 190
21
votes
11
replies
11k
views
Tool: Segemehl: A Fast One-Stop-Shop Mapping Tool
mapping next-gen
updated 10 months ago by 43k • written 11.6 years ago by 11k
21
votes
11
replies
2.8k
views
Tool: log / log.bio - keeping track of command line workflows
ac.gt log.bio log
updated 20 months ago by 43k • written 8.7 years ago by 13k
15
votes
11
replies
8.3k
views
Tool: Arriba: Fast and accurate gene fusion detection from RNA-Seq data
variant-calling RNA-Seq cancer gene-fusion
updated 11 months ago by 43k • written 6.3 years ago by ▴ 150
7
votes
11
replies
3.2k
views
Tool: Graphical User Interface for creating an automated RNA-Sequencing Pipeline via Kallisto and DESeq2
DESeq2 kallisto RNA-Seq
updated 10 months ago by 43k • written 5.4 years ago by ▴ 60
17
votes
11
replies
11k
views
6 follow
Tool: Pyfaidx: Efficient, "Pythonic" Random Access To Fasta Files Using Samtools-Compatible Indexing
fasta python samtools
updated 10 months ago by 43k • written 10.3 years ago by 10k
6
votes
10
replies
4.4k
views
Tool: Wham - a structural variant caller and association testing framework
genotype gwas bwa-mem bam structural-variant
updated 2.1 years ago by 43k • written 9.3 years ago by 12k
6
votes
10
replies
4.6k
views
Tool: Giant Virus Finder - discover giant virus sequences in metagenomes
Giant-Virus-Finder
updated 13 months ago by 43k • written 8.2 years ago by ▴ 350
11
votes
10
replies
2.3k
views
Tool: [Crushing the bureaucracy in bioinformatics] Introducing Skymap-JupyterHub: accessing and utilizing reprocessed expression/ allelic read count profil…
SNP RNA-Seq ChIP-Seq
updated 10 months ago by 43k • written 5.8 years ago by ▴ 300
3
votes
10
replies
1.7k
views
Tool: Quick & dirty DNA coordinates in any mac app
sequence alignment
updated 10 months ago by 43k • written 6.2 years ago by ▴ 180
7
votes
10
replies
1.5k
views
Tool: SamReadViewer - A small utility to visualise read alignment directly from sam format without reference.
samreadviewer
updated 11 months ago by 43k • written 3.6 years ago by 8.6k
23
votes
10
replies
12k
views
Tool: ggtree: phylogenetic tree visualization and annotation
ggtree phylogeny visualization
updated 10 months ago by 43k • written 7.9 years ago by ★ 2.6k
5
votes
10
replies
2.5k
views
Tool: Tools Section Now Enabled
meta biostars
updated 15 months ago by 43k • written 12.1 years ago by 100k
14
votes
10
replies
7.9k
views
Tool: ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization
ReactomePA R Visualization Pathway Bioconductor
updated 10 months ago by 43k • written 7.9 years ago by ★ 2.6k
8
votes
10
replies
7.2k
views
7 follow
Tool: Transcription Factor Binding Sites, Motifs and Expression Profiles from ~10200 ChIP-seq and ~20000 RNA-seq samples
ChIP-Seq transcription-factor miRNA lncRNA
updated 13 months ago by 43k • written 7.6 years ago by ▴ 860
17
votes
9
replies
17k
views
6 follow
Tool: ggrepel: repel overlapping text labels in ggplot2
R visualization
updated 11 months ago by 43k • written 8.4 years ago by ★ 2.3k
19
votes
9
replies
6.1k
views
Tool: Rlsim, A Package For Simulating Rna-Seq Library Preparation With Parameter Estimation
simulation rna-seq pcr illumina
updated 11 months ago by 43k • written 11.1 years ago by ★ 1.7k
3
votes
9
replies
3.6k
views
Tool: Download all refseq/genbank bacterial genomes from NCBI
genome sequencing
updated 10 months ago by 43k • written 7.3 years ago by ▴ 10
34
votes
9
replies
11k
views
7 follow
Tool: Bwa-Meth: Align And Tabulate Bs-Seq Reads
methylation
updated 10 months ago by 43k • written 10.2 years ago by 24k
7
votes
9
replies
4.0k
views
Tool: VCF-simplify: a VCF simplification tool.
VCF variants genome
updated 11 months ago by 43k • written 6.1 years ago by ★ 1.6k
4
votes
9
replies
2.7k
views
Tool: CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.3 years ago by • 0
17
votes
9
replies
6.1k
views
Tool: Pathomx: Metabolic Pathway Visualisation And Analysis
python pathway-visualization
updated 10 months ago by 43k • written 11.1 years ago by ▴ 180
16
votes
9
replies
8.7k
views
Tool: Introducing eLabFTW : free open source electronic lab notebook
eln open-source notebook-software
updated 2.4 years ago by 43k • written 9.7 years ago by ▴ 190
46
votes
9
replies
43k
views
7 follow
Tool: Tools to merge overlapping paired-end reads
ngs Assembly fastq
updated 13 months ago by ▴ 50 • written 7.5 years ago by ★ 1.2k
15
votes
9
replies
3.4k
views
Tool: FlexiDot: highly customizable, ambiguity-aware dotplots
dotplot visualization sequence-analysis
updated 10 months ago by 43k • written 6.0 years ago by ▴ 230
8
votes
9
replies
8.9k
views
Tool: Lofreq: A Fast And Sensitive Variant-Caller For Inferring Single-Nucleotide Variants From Ngs Data
snp next-gen somatic-variant
updated 10 months ago by 43k • written 11.6 years ago by ★ 2.5k
9
votes
9
replies
4.7k
views
Tool: pyCirclize - Circular visualization in Python
visualization circos matplotlib genome python
updated 9 months ago by • 0 • written 17 months ago by ▴ 150
12
votes
9
replies
7.8k
views
Tool: gogadget: an R package for go analysis visualization and interpretation
goseq R RNA-Seq gogadget
updated 10 months ago by 43k • written 7.8 years ago by 8.3k
2
votes
8
replies
3.7k
views
Tool: Mirnakey - A Software Pipeline For The Analysis Of Microrna Deep Sequencing Data
mirna
updated 10 months ago by 43k • written 11.7 years ago by 100k
3
votes
8
replies
737
views
Tool: Generate unit-tested, ready-to-run pipelines using natural language prompting
NGS pipeline genomics cloud AI
updated 3 months ago by 43k • written 3 months ago by ▴ 50
9
votes
8
replies
3.8k
views
6 follow
Tool: NCBI-SRA File Downloader
NCBI sra sequence
updated 14 months ago by 43k • written 8.7 years ago by ▴ 50
12
votes
8
replies
3.2k
views
Tool: BioBit: Global bioinformatics chat
communication
updated 13 months ago by 43k • written 7.9 years ago by ▴ 90
13
votes
8
replies
4.3k
views
Tool: MSigDB for Multiple Organisms in a Tidy Data Format
msigdb pathways R gsea
updated 11 months ago by 43k • written 6.1 years ago by 13k
8
votes
8
replies
2.9k
views
Tool: DiscoSnp++ 2.1.2 release: now genotypes and creates VCFs
SNP discosnp genotyping indel
updated 23 months ago by 43k • written 9.2 years ago by ▴ 900
15
votes
8
replies
2.4k
views
Tool: One Stop Solution for NGS Data Analysis
Predefined Robust NGS Analysis Tool
8.1 years ago by Persistent LABS ▴ 750
22
votes
8
replies
6.6k
views
Tool: BioTuring Browser: Making single-cell sequencing data in published studies really accessible!
scRNA-Seq single-cell
updated 10 months ago by 43k • written 5.6 years ago by ▴ 580
6
votes
8
replies
4.9k
views
Tool: Read-based phasing with WhatsHap
phasing
updated 10 months ago by 43k • written 7.4 years ago by ▴ 100
5
votes
8
replies
7.1k
views
6 follow
Tool: Converting MUMmer snps file to a real VCF file
VCF mummer SNP
updated 11 months ago by 43k • written 4.7 years ago by ★ 3.6k
8
votes
8
replies
3.2k
views
Tool: pyGeno 1.2: Python package for Personalized Genomics and Proteomics
python SNP rna-seq dbSNP ensembl
updated 23 months ago by 43k • written 9.1 years ago by ▴ 220
3
votes
8
replies
6.3k
views
Tool: MFEprimer-2.0: A Fast Thermodynamics-Based Program For Checking Pcr Primer Specificity
primer pcr
updated 10 months ago by 43k • written 12.0 years ago by ▴ 170
736 results • Page 2 of 15
Recent Votes
Answer: ChatGPT optimized for bioinformatics questions
Comment: ChatGPT optimized for bioinformatics questions
C: How can I perform Differential expression analysis with just one control and one
C: How can I perform Differential expression analysis with just one control and one
C: How can I perform Differential expression analysis with just one control and one
How can I perform Differential expression analysis with just one control and one cancer sample?
Comment: scRNAseq Differential expression analysis
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Recent Replies
Comment: how to treat the replicates while performing WGCNA by mavy ▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object by Alex Reynolds 35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF) by aidangcruickshank ▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data? by Ngrin • 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2 by swbarnes2 14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot by LauferVA 4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Answer: GG Sankey plot by bk11 ★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
Answer: Trimming tool by ntsopoul ▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
Answer: Trimming tool by GenoMax 142k
There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by bk11 ★ 2.5k
Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
Comment: Reconstruction of locus, order contigs by dthorbur ★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
Comment: how to treat the replicates while performing WGCNA by andres.firrincieli 3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
Comment: How to systematically check if a bam file is truncated by alanh ▴ 170
For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
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