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733 results • Page 2 of 15
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11
votes
14
replies
6.5k
views
6 follow
Tool: [share] Script to bulk retrieve DNA sequences by protein IDs from GenBank
python genbank sequence cds protein
updated 2.2 years ago by 43k • written 9.5 years ago by ▴ 130
21
votes
14
replies
9.4k
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 10 months ago by 43k • written 3.4 years ago by ★ 3.2k
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 10 months ago by 43k • written 3.2 years ago by ▴ 430
53
votes
13
replies
5.6k
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 8.9 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 12.0 years ago by 100k
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
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 2.5 years ago by 43k • written 9.9 years ago by 19k
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 6.5 years ago by ★ 2.5k
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
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 9.7 years ago by ▴ 900
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 10 months ago by 43k • written 6.2 years ago by ▴ 150
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
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 10.2 years ago by 10k
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 5.3 years ago by ▴ 60
21
votes
11
replies
2.8k
views
Tool: log / log.bio - keeping track of command line workflows
ac.gt log.bio log
updated 19 months ago by 43k • written 8.6 years ago by 13k
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
14
votes
10
replies
7.8k
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 7.8 years ago by ★ 2.6k
23
votes
10
replies
12k
views
Tool: ggtree: phylogenetic tree visualization and annotation
ggtree phylogeny visualization
updated 10 months ago by 43k • written 7.8 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 12 months ago by 43k • written 7.6 years ago by ▴ 860
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
7
votes
10
replies
1.5k
views
Tool: SamReadViewer - A small utility to visualise read alignment directly from sam format without reference.
samreadviewer
updated 10 months ago by 43k • written 3.6 years ago by 8.6k
5
votes
10
replies
2.5k
views
Tool: Tools Section Now Enabled
meta biostars
updated 14 months ago by 43k • written 12.0 years ago by 100k
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 5.7 years ago by ▴ 300
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
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 7.7 years ago by 8.3k
7
votes
9
replies
4.0k
views
Tool: VCF-simplify: a VCF simplification tool.
VCF variants genome
updated 10 months ago by 43k • written 6.0 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
46
votes
9
replies
43k
views
7 follow
Tool: Tools to merge overlapping paired-end reads
ngs Assembly fastq
updated 12 months ago by ▴ 50 • written 7.4 years ago by ★ 1.2k
15
votes
9
replies
3.3k
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
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
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
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
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
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 10 months ago by 43k • written 11.1 years ago by ★ 1.7k
17
votes
9
replies
17k
views
6 follow
Tool: ggrepel: repel overlapping text labels in ggplot2
R visualization
updated 10 months ago by 43k • written 8.3 years ago by ★ 2.3k
9
votes
8
replies
3.7k
views
6 follow
Tool: NCBI-SRA File Downloader
NCBI sra sequence
updated 13 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
3
votes
8
replies
716
views
Tool: Generate unit-tested, ready-to-run pipelines using natural language prompting
NGS pipeline genomics cloud AI
updated 12 weeks ago by 43k • written 12 weeks ago by ▴ 50
13
votes
8
replies
4.3k
views
Tool: MSigDB for Multiple Organisms in a Tidy Data Format
msigdb pathways R gsea
updated 10 months ago by 43k • written 6.1 years ago by 13k
8
votes
8
replies
4.4k
views
Tool: MetaR: a simple language useful for RNA-Seq data analysis
RNA-Seq R
updated 2.1 years ago by 43k • written 9.3 years ago by ▴ 170
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
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 22 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 11.9 years ago by ▴ 170
15
votes
8
replies
2.4k
views
Tool: One Stop Solution for NGS Data Analysis
Predefined Robust NGS Analysis Tool
8.0 years ago by Persistent LABS ▴ 750
22
votes
8
replies
6.5k
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
8
votes
8
replies
2.8k
views
Tool: DiscoSnp++ 2.1.2 release: now genotypes and creates VCFs
SNP discosnp genotyping indel
updated 23 months ago by 43k • written 9.1 years ago by ▴ 900
5
votes
8
replies
7.0k
views
6 follow
Tool: Converting MUMmer snps file to a real VCF file
VCF mummer SNP
updated 10 months ago by 43k • written 4.7 years ago by ★ 3.6k
733 results • Page 2 of 15
Recent Votes
Answer: Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
How to convert plink data from 38th assembly to 37
How to convert plink data from 38th assembly to 37
Comment: How to access TCGA samples that were treated with a specific drug?
Comment: Normalize scRNAseq data to housekeeping genes to compare several datasets
Comment: Converting CRAM to FastQ
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Recent Replies
Comment: How to access TCGA samples that were treated with a specific drug? by GenoMax 142k
It is possible that these drugs may not have been directly used in TCGA. Authors could have looked for mutations known to be acted on by th…
Comment: Does comparing two different groups to a common third group introduce bias in th by Qroid ▴ 40
Are you thinking about a specific scenario? If so, can you provide more info? I think the basic answer is that, yes, your choice of group C…
Answer: Bedtools merge minimum overlap? by harold.smith.tarheel ★ 4.9k
Bedtools [intersect][1] allows you to specify the fraction of overlap between two BED (or BAM) files using the F/f/r flags. You could split…
Comment: How to access TCGA samples that were treated with a specific drug? by Qroid ▴ 40
Sorry, I should have been more specific. By "that list" I mean what's populated in the Therapeutic Agents tab when no filters are applied. …
Comment: Bedtools merge minimum overlap? by bk11 ★ 2.4k
Not sure if you wanting to do like this- cat your_input.bed chr1 100 200 region1 + chr1 180 300 regi…
Comment: Extract gRNA sequence using cutadapt by GenoMax 142k
If you know what the boundaries of your construct look like then trim the left-end of the read using the tag on that end (`ktrim=l`). Then …
Comment: Extract gRNA sequence using cutadapt by gernophil ▴ 80
> Not every read in your data is going to match a guide. That is also true for sure. Let me clarify what I mean. For every read you should…
Answer: VG : No reference-sense paths available in the graph; falling back to generic pa by anovak ▴ 120
If your GFA has paths in it that are P lines with names that don't include a sample name, contig name, and separators, then those are what …
Comment: Extract gRNA sequence using cutadapt by GenoMax 142k
> if you look at a fastq file you should be able to tell for every read definitely, if it has a perfect match for a guide in it and what gu…
Answer: DiffBind: no peaks in DBA by jared.andrews07 ★ 16k
Because `dba.analyze` is not meant to be run directly on a peaks file. Have you read the documentation? In addition, a ChIP-seq experiment…
Comment: Converting CRAM to FastQ by Maverick ▴ 10
Thank you so much! Will look it up right away.
Comment: Extract gRNA sequence using cutadapt by gernophil ▴ 80
> I don't think every guide is supposed to show up in these experiments as far as I have seen. You will get some guides with 0 counts as yo…
Comment: Converting CRAM to FastQ by GenoMax 142k
Use `samtools view ` for this conversion. See discussion in https://www.biostars.org/p/9592860/ Specifically @jkbonfield's comment here --…
Comment: How to access TCGA samples that were treated with a specific drug? by GenoMax 142k
No that was only from Breast cancer. You could try selecting all data and see if you are able to see all treatments in the set. No idea a…
Comment: Extract gRNA sequence using cutadapt by GenoMax 142k
I don't think every guide is supposed to show up in these experiments as far as I have seen. You will get some guides with 0 counts as you …
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