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734 results • Page 1 of 15
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66
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Tool: Converting Nebula Genomics Data to 23andMe Format
23andMe Nebula
3 hours ago by Guillermo • 0
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
2
votes
0
replies
204
views
Tool: pySEACR
Peak-Calling CUT-and-RUN
25 days ago by Adam ▴ 30
2
votes
3
replies
493
views
Tool: DEGap - an online tool for Differential Gene Expression analysis
degap
27 days ago by Anastasia ▴ 10
2
votes
1
reply
363
views
Tool: TGSFilter, An ultra-fast and efficient tool for long reads filtering and trimming
genome-assembly filtering reads trimming
updated 6 weeks ago by • 0 • written 6 weeks ago by ▴ 190
0
votes
0
replies
231
views
Tool: MicrobiomePhylo: A Comprehensive Platform for Advanced Microbiome Amplicon Sequencing Data Analysis and Visualization
microbiome analysis data 16S
6 weeks ago by camillatafuro • 0
83
votes
46
replies
9.0k
views
15 follow
Tool: ChatGPT optimized for bioinformatics questions
gpt
updated 7 weeks ago by 4.2k • written 11 months ago by ▴ 840
5
votes
2
replies
2.5k
views
Tool: Coovar: Co-Occurring Variant Analyzer
snp variant-annotation
updated 8 weeks ago by 142k • written 11.5 years ago by ★ 3.0k
1
vote
4
replies
419
views
Tool: A c library for reading and writing sequences in fasta and fastq format.
seqio
8 weeks ago by dwpeng • 0
1
vote
0
replies
246
views
Tool: HFKReads, an ultra-fast and efficient tool for high frequency kmer sequencing reads extraction
kmer organelle metagenomic assembly
10 weeks ago by Huiyang ▴ 190
0
votes
0
replies
282
views
Tool: Microbiome Analysis: Comprehensive 16S Meta-barcoding Analysis in R with Phyloseq - On Sale Now!
R microbiome 16S phyloseq analysis
9 weeks ago by camillatafuro • 0
0
votes
0
replies
171
views
Tool: Annotating the epitope-specificity of TCRs with bioinformatics
Annotation TCR Epitope-specificity
11 weeks ago by tim • 0
10
votes
12
replies
1.8k
views
Tool: PanDepth, an ultra-fast and efficient genomic tool for coverage calculation
bam paf depth cram coverage
11 weeks ago by Huiyang ▴ 190
1
vote
0
replies
259
views
Tool: gxf2bed: A high-performance GTF/GFF-to-BED converter written in Rust
convert gff gtf bed
3 months ago by alejandrogzi ▴ 120
3
votes
8
replies
724
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
3
votes
0
replies
226
views
Tool: GW: fast genome browser and variant exploration tool
genome genomics variant-annotation genome-browser visualization
3 months ago by clealk ▴ 50
1
vote
0
replies
217
views
Tool: BIRCH3.90 - BioLegato, Apple Silicon, Updates
genomics sequence transcriptomics
3 months ago by brian.fristensky ▴ 460
0
votes
0
replies
210
views
Tool: Get `BPCells` with Bioconductor workflow
single cell BPCells
3 months ago by Yun • 0
1
vote
3
replies
663
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
273
views
Tool: tinybio in OpenAI App Store
gpt
3 months ago by Sasha ▴ 840
0
votes
0
replies
863
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
401
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
247
views
Tool: De Novo assembler (in C, supports MPI parallelism) available for experimenting with
de-novo trie olc
updated 5 months ago by 43k • written 5 months ago by ▴ 10
4
votes
0
replies
466
views
Tool: NOEL: An extremely fast Non-Overlapping Exon Length calculator written in Rust
gene-annotation exon-length
5 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
545
views
Tool: deepBreaks: a machine learning tool for identifying and prioritizing genotype-phenotype associations
python genetics
updated 6 months ago by 43k • written 6 months ago by • 0
1
vote
1
reply
401
views
Tool: Coremine Medical Introduction - connect - discover - share | explore and visualize associations
drug-target drug gene
updated 6 months ago by 43k • written 6 months ago by ▴ 20
0
votes
0
replies
243
views
Tool: massSight: A tool to combine LC-MS datasets
qc metabolomics omics R lc-ms
6 months ago by Chiraag • 0
0
votes
0
replies
280
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
321
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
378
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
597
views
Tool: Python and R without installing apps
Resources
updated 8 months ago by ▴ 290 • written 8 months ago by ▴ 20
0
votes
0
replies
294
views
Tool: MTMCSKAT package for GWAS with efficient resampling, parallelization
SKAT MTMC-SKAT
updated 8 months ago by 43k • written 8 months ago by ▴ 100
11
votes
2
replies
775
views
Tool: Pipeline Generator
gpt
updated 8 months ago by 4.2k • written 8 months ago by ▴ 840
13
votes
6
replies
5.2k
views
Tool: csvtk - a cross-platform, efficient, practical and pretty CSV/TSV toolkit
CSV Golang TSV
8 months ago by shenwei356 8.5k
3
votes
1
reply
821
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 9 months ago by ▴ 150
9
votes
9
replies
4.6k
views
Tool: pyCirclize - Circular visualization in Python
visualization circos matplotlib genome python
updated 9 months ago by • 0 • written 16 months ago by ▴ 150
0
votes
2
replies
7.8k
views
Tool: The script to install the required packages for gene expression analysis using DESeq2 for downstream analysis and visualization
R RNAseq installation DESeq2
9 months ago by Aditya naman • 0
1
vote
0
replies
581
views
Tool: Create realistic VCF genomic data in just a few lines of Python code
genomic linkage python vcf tool disequilibrium
9 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 10 months ago by ▴ 370 • written 10.5 years ago by • 0
3
votes
2
replies
783
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
505
views
Tool: tinybio added sources & chat history - (ChatGPT optimized for bioinformatics questions)
gpt
updated 6 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
372
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
856
views
Tool: Experiment Generator
gpt
updated 10 months ago by 4.2k • written 10 months ago by ▴ 840
0
votes
0
replies
499
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
476
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
987
views
Tool: web app for user-friendly analysis of 16S rRNA gene meta-barcoding NGS data - bacterial microbiome
qiime2 16s microbiome ngs
updated 12 months ago by 43k • written 12 months ago by • 0
1
vote
2
replies
863
views
Tool: Tinybio Slackbot - a large language model slackbot for bioinformatics
qa
12 months ago by Sasha ▴ 840
734 results • Page 1 of 15
Recent Votes
Comment: Which hg38 file?
Answer: Which hg38 file?
Answer: Where to get the following bed file?
How to save GRanges object to csv file
Answer: How to get proteins from GFF file resulted from MAKER annotation
Answer: Gene ontology and homologs
Comment: anRichment is missing
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Recent Replies
Comment: Understanding STAR output (Aligned.out.sam file) by GenoMax 142k
Refer to SAM alignment format: https://samtools.github.io/hts-specs/SAMv1.pdf Check section 1.4.
Answer: Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genom by LChart 3.9k
Step 1: Go to TCGA in the GDC and open the Cohort Builder https://portal.gdc.cancer.gov/analysis_page?app=CohortBuilder&tab=general Step …
Comment: Where to get the following bed file? by GenoMax 142k
SeqCap kits are discontinued. If you don't find the said file your will need to email Roche Support per this page: https://sequencing.roche…
Answer: Where to get the following bed file? by LChart 3.9k
UCSC maintains a list of exome probe sets and targets. You could check there: https://hgdownload.soe.ucsc.edu/gbdb/hg19/exomeProbesets/
Comment: How to compute TPM normalized values for TCGA miRNA data? by Ngrin • 0
Yes, I found some similar ideas on biostar repository. So you think the authors have done something wrong? And I should only consider CPM?
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by Chris Dean ▴ 390
It is difficult to answer how they were able to identify *S. hominis* without seeing the code or paper. To address your second question, i…
Comment: Problem with Seurat package in PercentageFeatureSet function by bk11 ★ 2.4k
Did you check where the `features.tsv.gz` file had Gene IDs or Ensembl IDs?
Answer: How to compute TPM normalized values for TCGA miRNA data? by dsull ★ 6.0k
TPM is irrelevant for miRNA-seq; CPM works fine. TPM tries to adjust for length effects by dividing by gene length (e.g. reducing the im…
Comment: Applying the metacell2 algorithm using python by Wayne ★ 2.0k
"I'm also unsure what qualifies as a lateral gene." The [README where you reference](https://metacells.readthedocs.io/en/latest/readme.htm…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by sovrappensiero ▴ 90
Ah, yes this makes sense! I knew this was an issue with, say, using kraken2 on shotgun metagenomic reads, but I don't have a lot of experi…
Comment: How to access TCGA samples that were treated with a specific drug? by Qroid ▴ 40
Thank you. Maybe it's best to confirm with the authors about how they're getting responder/non-responder labels. I'll do that now.
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by Chris Dean ▴ 390
If you sequenced a short hypervariable region, most of your sequence reads will not be able to be assigned to the species level. One possi…
Comment: anRichment is missing by GenoMax 142k
Consider emailing Dr. Horvath about this. Until enough people make him aware of this issue WGCNA "problem" is unlikely to get fixed.
Comment: anRichment is missing by Tatyana • 0
Unfortunately, there are only tutorials and codes for tutorials for WGCNA, not installation files for any their packages... :(
Comment: anRichment is missing by GenoMax 142k
See this link for the WGCNA documentation and code from Peter Langfelder : https://bioinformatics.stackexchange.com/questions/21885/where-t…
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