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521 results • Page 1 of 11
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79
votes
86
replies
32k
views
20 follow
Tool: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
clumpify storage bbmap pigz compression
updated 10 months ago by 43k • written 7.4 years ago by 20k
128
votes
83
replies
13k
views
8 follow
Tool: Lossless ALAPY Fastq Compressor (now for MacOS X with 10-20% improved speed and compression ratio)
lossless-fastq-compression fastq-compressor
updated 10 months ago by 43k • written 7.1 years ago by ★ 2.8k
362
votes
82
replies
144k
views
35 follow
Tool: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel next-gen ngs
updated 5 weeks ago by ▴ 290 • written 11.2 years ago by ★ 4.4k
72
votes
71
replies
31k
views
17 follow
Tool: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling
volcano-plot bioconductor ggplot2 ggrepel
updated 10 months ago by 43k • written 5.7 years ago by 87k
56
votes
52
replies
50k
views
12 follow
Tool: Gene Set Clustering based on Functional annotation (GeneSCF)
geneSCF Gene-Clustering
updated 10 months ago by 43k • written 9.7 years ago by 7.5k
61
votes
51
replies
22k
views
9 follow
Tool: Efficiently process (view, analize, clip ends, convert, demultiplex, dereplicate) SFF/FastQ files
sff sequence fastq next-gen
updated 10 months ago by 43k • written 10.0 years ago by ▴ 790
26
votes
50
replies
14k
views
8 follow
Tool: Retrieve a subset of FASTA from large Illumina multi-FASTA file
fasta multi-fasta illumina
updated 10 months ago by 43k • written 7.9 years ago by ▴ 50
83
votes
46
replies
8.9k
views
15 follow
Tool: ChatGPT optimized for bioinformatics questions
gpt
updated 7 weeks ago by 4.2k • written 11 months ago by ▴ 840
18
votes
39
replies
4.3k
views
Tool: CBioInfCpp.h as a C++ lib containing some functions for bioinformatics
cpp
updated 11 months ago by 43k • written 5.1 years ago by ▴ 50
231
votes
38
replies
146k
views
29 follow
Tool: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
ensembl genome-coordinates liftover
updated 10 months ago by 43k • written 11.2 years ago by 19k
31
votes
30
replies
15k
views
6 follow
Tool: BioVinci: user-friendly software to make plotting easy - PCA, 3D scatter plot, venn diagram, you name it.
gene RNA-Seq Venn-diagram PCA
updated 10 months ago by 43k • written 6.0 years ago by ▴ 450
18
votes
30
replies
10k
views
6 follow
Tool: Introducing FilterByTile: Remove Low-Quality Reads Without Adding Bias
Illumina BBMap filterbytile
updated 10 months ago by 43k • written 7.4 years ago by 20k
24
votes
26
replies
3.6k
views
Tool: ClinCNV: CNV detection from short reads
variant-calling cna cnv
updated 10 months ago by 43k • written 4.5 years ago by ★ 2.9k
17
votes
25
replies
2.4k
views
Tool: Platform for Bioinformatics Students, Scholars and Scientists
sequence genome
updated 10 months ago by 43k • written 8.2 years ago by ▴ 50
7
votes
25
replies
11k
views
6 follow
Tool: MIGEC: towards error-free profiling of immune repertoires
sequencing-error tcr antibody molecular-barcode
updated 10 months ago by 43k • written 10.0 years ago by 3.5k
13
votes
25
replies
11k
views
9 follow
Tool: Mitcr: A Software Tool For Analyzing T-Cell Receptor Sequencing Data
analysis sequencing ngs
updated 10 months ago by 43k • written 10.7 years ago by 3.5k
68
votes
25
replies
16k
views
12 follow
Tool: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
fastq SRA
updated 6 months ago by 142k • written 5.2 years ago by ★ 1.4k
48
votes
24
replies
8.2k
views
14 follow
Tool: Hera: A new tool for RNA-Seq analysis
kallisto RNA-Seq STAR gene-fusion
updated 10 months ago by 43k • written 6.8 years ago by ▴ 580
20
votes
23
replies
7.2k
views
6 follow
Tool: EaSeq - Interactive ChIP-seq analysis and visualization (for Windows)
easeq Windows Visualization ChIP-Seq
updated 10 months ago by 43k • written 8.1 years ago by ▴ 460
56
votes
23
replies
5.1k
views
10 follow
Tool: ASCIIGenome: Text Only Genome Viewer!
terminal genome-browser java ASCIIGenome
updated 10 months ago by 43k • written 7.8 years ago by 14k
31
votes
22
replies
13k
views
6 follow
Tool: SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
FASTQ SeqKit FASTA
updated 10 months ago by 43k • written 7.6 years ago by 8.5k
9
votes
22
replies
9.7k
views
Tool: BioLabDonkey - new Mac program for molecular biologists
software biolabdonkey
10 months ago by vytarasov ▴ 180
26
votes
22
replies
13k
views
10 follow
Tool: BBSketch - A Tool for Rapid Sequence Comparison
minhash sketch bbmap blast
updated 11 months ago by 43k • written 7.2 years ago by 20k
18
votes
21
replies
4.4k
views
Tool: uQ - small binary FASTQ
Compression FASTQ
updated 10 months ago by 43k • written 7.2 years ago by 13k
38
votes
21
replies
19k
views
8 follow
Tool: pybam - 100% python BAM reader
python htspython bam pysam
updated 10 months ago by 43k • written 8.1 years ago by 13k
29
votes
20
replies
3.7k
views
Tool: FastQt : a clone of FastQC in C++/Qt
fastqc Cpp fastq Qt
updated 10 months ago by 43k • written 7.4 years ago by ★ 2.4k
22
votes
20
replies
4.8k
views
Tool: elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMtools for processing SAM/BAM files
sam bam bqsr
updated 10 months ago by 43k • written 5.5 years ago by ▴ 150
15
votes
19
replies
8.7k
views
6 follow
Tool: Gemini: Integrative Exploration Of Genetic Variation And Genome Annotations
vcf database genome variation
updated 10 months ago by 43k • written 11.0 years ago by 12k
25
votes
19
replies
8.2k
views
10 follow
Tool: pathfindR - Enrichment Analysis using Active Subnetworks
subnetwork R pathway-enrichment
updated 10 months ago by 43k • written 6.1 years ago by ★ 1.3k
38
votes
19
replies
11k
views
Tool: Excel add-in for DNA/RNA string manipulations
sequence DNA RNA Excel
updated 10 months ago by 43k • written 8.2 years ago by ▴ 140
23
votes
19
replies
4.3k
views
7 follow
Tool: Big Browser : a new genom browser in development
genome-browser
updated 10 months ago by 43k • written 8.2 years ago by ★ 2.4k
7
votes
17
replies
5.1k
views
Tool: SPLiT-Seq Demultiplexing a bash tool for extraction of barcoded single cells
RNA-Seq sequencing
updated 10 months ago by 43k • written 5.6 years ago by ▴ 80
28
votes
17
replies
5.1k
views
7 follow
Tool: PCAtools: everything Principal Components Analysis
eigenvector pca bioconductor R
updated 10 months ago by 43k • written 5.2 years ago by 87k
22
votes
17
replies
4.0k
views
Tool: epic: new ChIP-Seq caller based on the SICER algorithm
ChIP-Seq
updated 10 months ago by 43k • written 8.1 years ago by ▴ 960
6
votes
16
replies
2.9k
views
Tool: MicroScope: ChIP-seq and RNA-seq software analysis suite for gene expression heatmaps
RNA-Seq ChIP-Seq
updated 10 months ago by 43k • written 7.6 years ago by ▴ 350
8
votes
16
replies
2.9k
views
Tool: CuteVcf : A Qt application to view VCF file
htslib gui vcf tabix Qt
updated 10 months ago by 43k • written 7.4 years ago by ★ 2.4k
50
votes
16
replies
14k
views
12 follow
Tool: Omictools: A didactic directory for omic data analysis (NGS, microarray, PCR, MS, NMR)
pcr software ngs
updated 10 months ago by 43k • written 10.6 years ago by ▴ 450
16
votes
16
replies
7.6k
views
6 follow
Tool: Oncofuse: Prediction Of Driver Gene Fusions From Ngs Data
annotation fusion rna-seq ngs
updated 10 months ago by 43k • written 10.7 years ago by 3.5k
30
votes
15
replies
10k
views
7 follow
Tool: Snakemake--Python-Based Workflow Management
workflow snakemake python
updated 10 months ago by 43k • written 10.4 years ago by 26k
76
votes
14
replies
13k
views
10 follow
Tool: karyoploteR: uncircle your genomes
karyoploteR Rdataviz NGS
updated 10 months ago by 43k • written 6.9 years ago by ★ 3.4k
13
votes
14
replies
2.3k
views
Tool: Collaboration on an empirical QC tool
RNA-Seq QC sequencing
updated 10 months ago by 43k • written 7.0 years ago by 54k
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
13
votes
14
replies
6.1k
views
9 follow
Tool: open-cravat: variant annotation tool
open-cravat
updated 10 months ago by 43k • written 5.4 years ago by ▴ 260
19
votes
14
replies
8.2k
views
7 follow
Tool: AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
PolyG Quality-Control Filtering Fastq AfterQC
updated 10 months ago by 43k • written 8.0 years ago by ★ 2.5k
7
votes
14
replies
16k
views
7 follow
Tool: Art: Simulation Tools To Generate Synthetic Next-Generation Sequencing Reads.
sequence
updated 10 months ago by 43k • written 11.8 years ago by 100k
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
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
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
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
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
521 results • Page 1 of 11
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: 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 …
Comment: Extract gRNA sequence using cutadapt by gernophil ▴ 80
> Can you try lowering the k to k=9? Wouldn't that mess with the results since all my kmers are 20bp? > You don't have any duplicate sequ…
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