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733 results • Page
1 of 15
Sort: Votes
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Views
Votes
Replies
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
jena
▴ 290 • written 11.2 years ago by
ole.tange
★ 4.4k
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
Ram
43k • written 11.2 years ago by
Malachi Griffith
19k
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
Ram
43k • written 7.1 years ago by
Petr Ponomarenko
★ 2.8k
83
votes
46
replies
8.8k
views
15 follow
Tool:
ChatGPT optimized for bioinformatics questions
gpt
updated 6 weeks ago by
LauferVA
4.2k • written 10 months ago by
Sasha
▴ 840
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
Ram
43k • written 7.4 years ago by
Brian Bushnell
20k
76
votes
14
replies
13k
views
10 follow
Tool:
karyoploteR: uncircle your genomes
karyoploteR
Rdataviz
NGS
updated 10 months ago by
Ram
43k • written 6.9 years ago by
bernatgel
★ 3.4k
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
Ram
43k • written 5.7 years ago by
Kevin Blighe
87k
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
GenoMax
141k • written 5.2 years ago by
Phil Ewels
★ 1.4k
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
Ram
43k • written 10.0 years ago by
BioApps
▴ 790
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
Ram
43k • written 9.7 years ago by
EagleEye
7.5k
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
Ram
43k • written 7.8 years ago by
dariober
14k
54
votes
13
replies
10k
views
6 follow
Tool:
Bedtools: Analyzing Genomic Features
bedtools
updated 10 months ago by
Ram
43k • written 12.0 years ago by
Istvan Albert
100k
54
votes
7
replies
4.0k
views
6 follow
Tool:
Looking For People That Would Try A Custom Genome Viewer That I Wrote For Bioinformatics
genome-viewer
updated 10 months ago by
Ram
43k • written 10.9 years ago by
chbelhumeur2000
▴ 40
53
votes
6
replies
9.7k
views
8 follow
Tool:
list of dockerized bioinformatics apps
docker
updated 2.2 years ago by
Ram
43k • written 9.5 years ago by
14134125465346445
★ 3.6k
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 15 months ago by
Ram
43k • written 8.9 years ago by
Daniel
★ 4.0k
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
Ram
43k • written 10.6 years ago by
arnaud.desfeux
▴ 450
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
Ram
43k • written 6.8 years ago by
sonpham
▴ 580
46
votes
9
replies
43k
views
7 follow
Tool:
Tools to merge overlapping paired-end reads
ngs
Assembly
fastq
updated 12 months ago by
Charles-Alexandre Roy
▴ 50 • written 7.4 years ago by
Abdul Rafay Khan
★ 1.2k
38
votes
19
replies
11k
views
Tool:
Excel add-in for DNA/RNA string manipulations
sequence
DNA
RNA
Excel
updated 10 months ago by
Ram
43k • written 8.1 years ago by
jgbaum
▴ 140
38
votes
21
replies
19k
views
8 follow
Tool:
pybam - 100% python BAM reader
python
htspython
bam
pysam
updated 10 months ago by
Ram
43k • written 8.0 years ago by
John
13k
34
votes
30
replies
2.9k
views
6 follow
Tool:
BioFlows - Container-enabled Bioinformatics pipeline engine
workflow
next-gen
RNA-Seq
pipeline
updated 13 months ago by
Ram
43k • written 3.4 years ago by
drsami
▴ 90
34
votes
9
replies
11k
views
7 follow
Tool:
Bwa-Meth: Align And Tabulate Bs-Seq Reads
methylation
updated 10 months ago by
Ram
43k • written 10.2 years ago by
brentp
24k
33
votes
3
replies
15k
views
Tool:
Aligning Sequence Reads, Clone Sequences And Assembly Contigs With Bwa-Mem
bwa
ngs
updated 10 months ago by
Ram
43k • written 11.1 years ago by
lh3
33k
32
votes
6
replies
12k
views
Tool:
FASTA and FASTQ tools
Cpp
FASTA
Python
FASTQ
updated 15 months ago by
Ram
43k • written 8.9 years ago by
Kamil
★ 2.3k
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
Ram
43k • written 5.9 years ago by
Jennifer Pham
▴ 450
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
Ram
43k • written 7.6 years ago by
shenwei356
8.4k
30
votes
15
replies
10k
views
7 follow
Tool:
Snakemake--Python-Based Workflow Management
workflow
snakemake
python
updated 10 months ago by
Ram
43k • written 10.4 years ago by
Sean Davis
26k
29
votes
29
replies
3.5k
views
6 follow
Tool:
weld (former brew) - yet another fastq utility
illlumina
python
updated 21 months ago by
Ram
43k • written 8.2 years ago by
tinysnippets
▴ 40
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
Ram
43k • written 7.4 years ago by
sacha
★ 2.4k
28
votes
4
replies
15k
views
Tool:
Plotting GSEA output in R
RNA-Seq
javaGSEA
GSEA
updated 10 months ago by
Ram
43k • written 7.7 years ago by
thomaskuilman
▴ 850
28
votes
7
replies
11k
views
Tool:
Quast Is A Convenient Tool For Assembly Evaluation
assembly
quality
updated 10 months ago by
Ram
43k • written 11.2 years ago by
Nikolay Vyahhi
★ 1.3k
28
votes
17
replies
5.0k
views
7 follow
Tool:
PCAtools: everything Principal Components Analysis
eigenvector
pca
bioconductor
R
updated 10 months ago by
Ram
43k • written 5.2 years ago by
Kevin Blighe
87k
27
votes
5
replies
1.9k
views
6 follow
Tool:
Efficient querying of genomic reference databases with gget
ensembl
enrichr
ncbi
gget
uniprot
updated 23 months ago by
Lior Pachter
▴ 700 • written 23 months ago by
Laura Luebbert
▴ 450
27
votes
6
replies
16k
views
Tool:
Bioawk - Fasta, Fastq, Sam, Bed, Gff Aware Awk Programming
awk
updated 10 months ago by
Ram
43k • written 11.8 years ago by
Istvan Albert
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
Ram
43k • written 7.8 years ago by
WouterDeCoster
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
Ram
43k • written 9.9 years ago by
Malachi Griffith
19k
26
votes
4
replies
5.3k
views
Tool:
Dgidb - Mining The Druggable Genome
dgidb
drug-gene-interaction
updated 10 months ago by
Ram
43k • written 10.5 years ago by
Obi Griffith
20k
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
Ram
43k • written 7.9 years ago by
hcwang
▴ 50
26
votes
4
replies
3.3k
views
Tool:
LabWorm - a new CrowdSourcing platform for finding the newest & best bioinformatic tools
LabWorm
updated 12 months ago by
Ram
43k • written 7.9 years ago by
roy.granit
▴ 880
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
Ram
43k • written 7.2 years ago by
Brian Bushnell
20k
25
votes
17
replies
17k
views
Tool:
HeatmapGenerator: High performance RNAseq and microarray visualization software suite to examine differential gene expression levels using an R and C…
heatmap
microarray
R
Cpp
RNA-Seq
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
Bohdan Khomtchouk
▴ 350
25
votes
3
replies
4.9k
views
Tool:
Quick statistics from the command line
statistics
C
updated 16 months ago by
Ram
43k • written 8.8 years ago by
Kamil
★ 2.3k
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
Ram
43k • written 6.1 years ago by
egeulgen
★ 1.3k
24
votes
26
replies
3.6k
views
Tool:
ClinCNV: CNV detection from short reads
variant-calling
cna
cnv
updated 10 months ago by
Ram
43k • written 4.5 years ago by
German.M.Demidov
★ 2.9k
23
votes
10
replies
12k
views
Tool:
ggtree: phylogenetic tree visualization and annotation
ggtree
phylogeny
visualization
updated 10 months ago by
Ram
43k • written 7.8 years ago by
Guangchuang Yu
★ 2.6k
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
Ram
43k • written 8.1 years ago by
sacha
★ 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
Ram
43k • written 5.5 years ago by
Charlotte.Herzeel
▴ 150
22
votes
5
replies
8.4k
views
Tool:
Salmon: A fast and versatile new tool for RNA-seq quantification
RNA-Seq
updated 2.1 years ago by
Ram
43k • written 9.4 years ago by
Rob
6.5k
22
votes
4
replies
8.6k
views
Tool:
Very Bad Things
python
text
updated 16 months ago by
Ram
43k • written 11.2 years ago by
brentp
24k
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
Ram
43k • written 5.6 years ago by
sonpham
▴ 580
733 results • Page
1 of 15
Recent Votes
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
How do I find out the read lenght of a fastq file?
Calculate Allele balance by sample
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
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rohitsatyam102
▴ 850
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▴ 10
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35k
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Comment: Source other conda environments in a nextflow pipeline when nextflow itself is i
by
Arup Ghosh
3.2k
Use the standalone version of Nextflow and specify the process-specific conda environments paths.
Comment: gvcf joint calling
by
Jeremy Leipzig
22k
can you show us an exonic position in your VCF file that is all `./.`?
Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
by
O.rka
▴ 710
Thank you. This answers my question. The reason I am asking is because I’m trying to do set enrichment analysis with BRENDA pathways using…
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
by
colindaven
6.4k
I used to use nextflow in a conda env. That requires the env to be active when a pipeline is started. Also I have productive pipelines whic…
Comment: different FeatureCounts output for the same data
by
Istvan Albert
100k
just to clarify, it is not that the program algorithm works differently but the meaning of the flags changed; before -p was sufficient to…
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…
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