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733 results • Page 1 of 15
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4
votes
9
replies
2.6k
views
Tool: CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.2 years ago by • 0
2
votes
0
replies
190
views
Tool: pySEACR
Peak-Calling CUT-and-RUN
13 days ago by Adam ▴ 20
2
votes
3
replies
463
views
Tool: DEGap - an online tool for Differential Gene Expression analysis
degap
16 days ago by Anastasia ▴ 10
2
votes
1
reply
347
views
Tool: TGSFilter, An ultra-fast and efficient tool for long reads filtering and trimming
genome-assembly filtering reads trimming
updated 4 weeks ago by • 0 • written 4 weeks ago by ▴ 190
0
votes
0
replies
224
views
Tool: MicrobiomePhylo: A Comprehensive Platform for Advanced Microbiome Amplicon Sequencing Data Analysis and Visualization
microbiome analysis data 16S
4 weeks ago by camillatafuro • 0
83
votes
46
replies
8.8k
views
15 follow
Tool: ChatGPT optimized for bioinformatics questions
gpt
updated 6 weeks ago by 4.2k • written 10 months ago by ▴ 840
5
votes
2
replies
2.5k
views
Tool: Coovar: Co-Occurring Variant Analyzer
snp variant-annotation
updated 6 weeks ago by 141k • written 11.5 years ago by ★ 3.0k
1
vote
4
replies
400
views
Tool: A c library for reading and writing sequences in fasta and fastq format.
seqio
7 weeks ago by dwpeng • 0
1
vote
0
replies
233
views
Tool: HFKReads, an ultra-fast and efficient tool for high frequency kmer sequencing reads extraction
kmer organelle metagenomic assembly
8 weeks ago by Huiyang ▴ 190
0
votes
0
replies
272
views
Tool: Microbiome Analysis: Comprehensive 16S Meta-barcoding Analysis in R with Phyloseq - On Sale Now!
R microbiome 16S phyloseq analysis
7 weeks ago by camillatafuro • 0
0
votes
0
replies
161
views
Tool: Annotating the epitope-specificity of TCRs with bioinformatics
Annotation TCR Epitope-specificity
10 weeks ago by tim • 0
10
votes
12
replies
1.7k
views
Tool: PanDepth, an ultra-fast and efficient genomic tool for coverage calculation
bam paf depth cram coverage
9 weeks ago by Huiyang ▴ 190
1
vote
0
replies
243
views
Tool: gxf2bed: A high-performance GTF/GFF-to-BED converter written in Rust
convert gff gtf bed
11 weeks ago by alejandrogzi ▴ 120
3
votes
8
replies
682
views
Tool: Generate unit-tested, ready-to-run pipelines using natural language prompting
NGS pipeline genomics cloud AI
updated 11 weeks ago by 43k • written 11 weeks ago by ▴ 50
3
votes
0
replies
213
views
Tool: GW: fast genome browser and variant exploration tool
genome genomics variant-annotation genome-browser visualization
11 weeks ago by clealk ▴ 50
1
vote
0
replies
209
views
Tool: BIRCH3.90 - BioLegato, Apple Silicon, Updates
genomics sequence transcriptomics
3 months ago by brian.fristensky ▴ 460
0
votes
0
replies
198
views
Tool: Get `BPCells` with Bioconductor workflow
single cell BPCells
3 months ago by Yun • 0
1
vote
3
replies
644
views
Tool: retroSeeker: discovering a large set of retrotransposons in humans and any species
Mobile-element Evolution Retrotransposon
3 months ago by lsp03yjh ▴ 860
1
vote
0
replies
260
views
Tool: tinybio in OpenAI App Store
gpt
3 months ago by Sasha ▴ 840
0
votes
0
replies
852
views
Tool: What do you think about Tfinder? a tool to find individual motifs in DNA sequence. Help us ameliorate
Motifs Transcription-factor
updated 4 months ago by 43k • written 4 months ago by • 0
0
votes
2
replies
381
views
Tool: Dot_plot_like_in_BLAST, a standalone tool for making dot plots similar to what online BLAST makes
Megablast Blastn dot plot dotplot BLAST
updated 4 months ago by 43k • written 4 months ago by ★ 1.2k
1
vote
0
replies
240
views
Tool: De Novo assembler (in C, supports MPI parallelism) available for experimenting with
de-novo trie olc
updated 4 months ago by 43k • written 4 months ago by ▴ 10
4
votes
0
replies
457
views
Tool: NOEL: An extremely fast Non-Overlapping Exon Length calculator written in Rust
gene-annotation exon-length
4 months ago by alejandrogzi ▴ 120
9
votes
4
replies
2.3k
views
Tool: SEDA (SEquence DAtaset builder): a desktop tool for processing FASTA files containing DNA and protein sequences
fasta sequences java
5 months ago by Hugo ▴ 380
0
votes
0
replies
535
views
Tool: deepBreaks: a machine learning tool for identifying and prioritizing genotype-phenotype associations
python genetics
updated 5 months ago by 43k • written 5 months ago by • 0
1
vote
1
reply
383
views
Tool: Coremine Medical Introduction - connect - discover - share | explore and visualize associations
drug-target drug gene
updated 5 months ago by 43k • written 5 months ago by ▴ 20
0
votes
0
replies
233
views
Tool: massSight: A tool to combine LC-MS datasets
qc metabolomics omics R lc-ms
5 months ago by Chiraag • 0
0
votes
0
replies
271
views
Tool: Coremine Medical used in study to discover differentially expressed genes in multiple sclerosis
drugs drug-targets genes
5 months ago by Coremine Medical ▴ 20
0
votes
0
replies
309
views
Tool: Introducing SpectraView - a tool to transform your literature reviews!
gene protein drug-discovery
updated 6 months ago by 43k • written 6 months ago by • 0
4
votes
0
replies
361
views
Tool: MyBrain-Seq: A Pipeline for MiRNA-Seq Data Analysis in Neuropsychiatric Disorders
mybrain-seq miRNA-seq pipeline neuropsychiatry docker
6 months ago by dannyzimm ▴ 50
12
votes
4
replies
1.1k
views
Tool: BBTools 39.03 released!
BBTools BBMap
6 months ago by Brian Bushnell 20k
2
votes
2
replies
586
views
Tool: Python and R without installing apps
Resources
updated 7 months ago by ▴ 290 • written 7 months ago by ▴ 20
0
votes
0
replies
289
views
Tool: MTMCSKAT package for GWAS with efficient resampling, parallelization
SKAT MTMC-SKAT
updated 7 months ago by 43k • written 7 months ago by ▴ 100
11
votes
2
replies
760
views
Tool: Pipeline Generator
gpt
updated 8 months ago by 4.2k • written 8 months ago by ▴ 840
13
votes
6
replies
5.1k
views
Tool: csvtk - a cross-platform, efficient, practical and pretty CSV/TSV toolkit
CSV Golang TSV
8 months ago by shenwei356 8.4k
3
votes
1
reply
784
views
Tool: pyGenomeViz - A genome visualization python package for comparative genomics
genome comparative-genomics python microbial-genomics visualization
updated 3 months ago by ▴ 90 • written 8 months ago by ▴ 150
9
votes
9
replies
4.6k
views
Tool: pyCirclize - Circular visualization in Python
visualization circos matplotlib genome python
updated 8 months ago by • 0 • written 16 months ago by ▴ 150
0
votes
2
replies
7.4k
views
Tool: The script to install the required packages for gene expression analysis using DESeq2 for downstream analysis and visualization
R RNAseq installation DESeq2
8 months ago by Aditya naman • 0
1
vote
0
replies
563
views
Tool: Create realistic VCF genomic data in just a few lines of Python code
genomic linkage python vcf tool disequilibrium
8 months ago by Rémy ▴ 10
1
vote
2
replies
3.5k
views
Tool: How Study Aromatic-Aromatic Interactions And Amino-Aromatic Interactions Of Protein-Ligands Complexes In The Pdb.
pdb
updated 9 months ago by ▴ 370 • written 10.5 years ago by • 0
3
votes
2
replies
766
views
Tool: Launched: Genozip 15 with co-compression of BAM and FASTQ
BAM CRAM compression FASTQ
updated 10 months ago by ▴ 300 • written 10 months ago by ▴ 230
0
votes
1
reply
492
views
Tool: tinybio added sources & chat history - (ChatGPT optimized for bioinformatics questions)
gpt
updated 4 weeks ago by • 0 • written 10 months ago by ▴ 840
7
votes
4
replies
2.9k
views
Tool: TreeView3 - An update to java TreeView
TreeView3 java
updated 8 months ago by ▴ 10 • written 5.8 years ago by ▴ 180
0
votes
0
replies
362
views
Tool: Unleashing the Power of Custom NGS Software for Cutting-Edge Research
DNAseq pipeline bisulfiteSeq RNAseq
updated 10 months ago by 13k • written 10 months ago by 11k
5
votes
3
replies
838
views
Tool: Experiment Generator
gpt
updated 10 months ago by 4.2k • written 10 months ago by ▴ 840
0
votes
0
replies
490
views
Tool: Easy API For Running Bioinformatics Jobs Via Python In The Cloud
api execution
11 months ago by Sasha ▴ 840
0
votes
0
replies
459
views
Tool: Single-cell RNA-seq data analysis tool Cellenics®
single-cell RNA-seq scRNA-seq
updated 11 months ago by 43k • written 11 months ago by • 0
0
votes
1
reply
974
views
Tool: web app for user-friendly analysis of 16S rRNA gene meta-barcoding NGS data - bacterial microbiome
qiime2 16s microbiome ngs
updated 11 months ago by 43k • written 11 months ago by • 0
1
vote
2
replies
848
views
Tool: Tinybio Slackbot - a large language model slackbot for bioinformatics
qa
11 months ago by Sasha ▴ 840
0
votes
0
replies
447
views
Tool: shinyCircos-V2.0: leveraging the creation of Circos plot with enhanced usability and advanced features
shinyCircos visualization Circular Circos genome
11 months ago by Andrewoods ▴ 110
733 results • Page 1 of 15
Recent Votes
Comment: alignment result
Comment: clustalo - align milions of short seq, memory issue
Answer: clustalo - align milions of short seq, memory issue
Comment: downloading genomes in fasta format from accession ids
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
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Recent Replies
Comment: Highest variable features in single cell data by ATpoint 82k
> and these cells are not even in a single cluster. What does this mean? If you run clustering on all cells then every cell is assigned t…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas by Bertalan_Takacs ▴ 90
Yes, I can tell that, but as far as I see it doesn't contain any other information about the genomes, such as if they were representative i…
Answer: Hide positions in alignment with 99% "–" characters to ignore single sequence in by b.contreras.moreira ▴ 170
You can try <https://github.com/inab/trimal>
Comment: To get p-values for the TPM by VITALA • 0
yes i want what rsem does and i did try with prior-enhanced option/pRSEM, but i think pRSEM is for chipseq data
Comment: alignment result by ahmad.sajad4541 • 0
Thank you so much. Should i proceed for annotation step?
Comment: PCA plot (Suggestions Needed) by swbarnes2 14k
The code you already posted in the bioconductor board had simulated data, and the PCA image is the same.
Answer: Network Alignment by Scooter ▴ 280
Unfortunately, it's not working for me either, and the web site doesn't exist anymore. You might try reaching out to the authors, but I kn…
Answer: How could I generate a gi_taxid_nucl.dmp file similar to the one previously host by ZhangYuanfeng • 0
JUST GIVE THE ANSWER! Here is the solution: ```bash aria2c -c -s 4 -j 4 \ https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/pd…
Comment: PCA plot (Suggestions Needed) by Aaliya ▴ 10
I have actually used DESeq2 data.
Comment: Why cd-hit-est not work when sequence identity threshold<0.95？ by Dateline • 0
So, why? I have 18GB of data, and when -c=0.95, the run ends in about two days, while when -c=0.9, it has been three days and only a little…
Answer: Heatmap and rna-seq by Kevin Blighe 87k
Hi, you can take the list of GSEA pathways and then use these via GSVA (https://github.com/rcastelo/GSVA) to create a heatmap. You hav…
Comment: Clustering of DAVID gene enrichment results from gene expression studies by Kevin Blighe 87k
You will have to elaborate on what is the error
Comment: clustalo - align milions of short seq, memory issue by emmanouil.a ▴ 120
Hi GenoMax and Mensur Dlakic, thank you for your feedback. I'm changing approach in the way to work with a smaller number of seq.
Comment: Annovar using R package by Pierre Lindenbaum 161k
duplicate of your previous question: https://www.biostars.org/p/9592646/ why using R when there are shell-based tools like VEP ? slivar , …
Comment: Trouble with Pilon installation by Lissa Cruz Saavedra • 0
Hi I am trying to install the software but I didn't find the way to clone from github. Could you help me with the pipeline of instruction…
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