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521 results • Page 1 of 11
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79
votes
86
replies
31k
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 4 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
8.8k
views
15 follow
Tool: ChatGPT optimized for bioinformatics questions
gpt
updated 6 weeks ago by 4.2k • written 10 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 5.0 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
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 7.3 years ago by 20k
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 5.9 years ago by ▴ 450
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
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 141k • written 5.2 years ago by ★ 1.4k
7
votes
25
replies
10k
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
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
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
5.0k
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 8.4k
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
9
votes
22
replies
9.7k
views
Tool: BioLabDonkey - new Mac program for molecular biologists
software biolabdonkey
9 months ago by vytarasov ▴ 180
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 8.0 years ago by 13k
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
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
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 8.1 years ago by ★ 2.4k
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 8.1 years ago by ▴ 140
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
22
votes
17
replies
3.9k
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
28
votes
17
replies
5.0k
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
521 results • Page 1 of 11
Recent Votes
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
Answer: Is there a tool that sorts gtf files?
Answer: gvcf joint calling
Answer: Heatmap and rna-seq
Answer: How to use limma to find differentially expressed genes in response to a continu
A: Blast Settings For Short Sequences
A: Blast Settings For Short Sequences
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Popular Question to rohitsatyam102 ▴ 850
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Recent Replies
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by BioinfGuru ★ 1.7k
Thanks Ram. Using merge maxed out my ram on a large list, but your suggestion directed me to purrr::reduce which works great.
Comment: ScRNA data question by starswillfade ▴ 10
features <- SelectIntegrationFeatures(object.list = merged_dat) data.anchors <- FindIntegrationAnchors(object.list = merged_dat, …
Comment: gvcf joint calling by zihanss • 0
Thank you for your help! I really appreciate it! And you know, the merged WES gVCF files still have "NA" loci. For such cases, I am quite …
Comment: Correct way to compare multiple treaments between RNA-Seq samples using edgeR? by Guille • 0
Thank you for your answer! The MDS plot seems to group most treatment groups close-by, so I'm starting to suspect the effect of treatment …
Answer: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC: by Mensur Dlakic ★ 27k
They say that we remember better things we figured out on our own, rather than things we were taught. You were literally two clicks away fr…
Comment: Heatmap and rna-seq by dsull ★ 5.8k
https://maayanlab.cloud/clustergrammer/ It's a web-based tool (can also be a python jupyter widget) that I find useful for exploring a pat…
Answer: Limma Analysis Agilent Microarray Data (GPL1708) by Gordon Smyth ★ 7.0k
There is an Agilent array case study in the limma User's Guide, which you might find helpful and somewhat simpler. I don't recommend col…
Answer: Correct way to compare multiple treaments between RNA-Seq samples using edgeR? by Gordon Smyth ★ 7.0k
The comparison you've done seems exactly right to test whether treatment 2 modifies or enhances the effect of treatment 1. Have you exam…
Answer: How to use limma to find differentially expressed genes in response to a continu by Gordon Smyth ★ 7.0k
There's no need for form a contrast because the score variable is already in the model. A continuous variable is its own contrast. Just run…
Comment: Create a new bed file with all pairwise combinations between two other bed files by J ▴ 10
Oh wow, bedops closest-features, how did I overlook that!! I didn't know about it; thank you! Your awk script is beautiful. This worked per…
Comment: Create a new bed file with all pairwise combinations between two other bed files by J ▴ 10
Thank you Pierre! I'll try this out with my full data set.
Answer: DNA methylation preprocessing by cao510927 ▴ 30
I happend to see one paper doing the similar thing, share it with you guys, "A systematic evaluation of normalization methods and probe rep…
Answer: Create a new bed file with all pairwise combinations between two other bed files by Alex Reynolds 35k
I think Pierre's answer might be correct for your test input, but it doesn't account for the start position of the reference element and so…
Comment: Highest variable features in single cell data by bk11 ★ 2.4k
You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
Comment: Heatmap and rna-seq by GenoMax 141k
Please include a link when you are recommending a tool. There can be programs with similar names.
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