Limit : all time
all time today this week this month this year
733 results • Page 1 of 15
Sort: Votes
Rank 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 29 days ago by ▴ 290 • written 11.2 years ago by ★ 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 43k • written 11.2 years ago by 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 43k • written 7.1 years ago by ★ 2.8k
83
votes
46
replies
8.7k
views
15 follow
Tool: ChatGPT optimized for bioinformatics questions
gpt
updated 5 weeks ago by 4.2k • written 10 months ago by ▴ 840
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
76
votes
14
replies
12k
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
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 5.6 years ago by 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 141k • written 5.2 years ago by ★ 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 43k • written 10.0 years ago by ▴ 790
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
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
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 43k • written 10.9 years ago by ▴ 40
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
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 43k • written 8.9 years ago by ★ 4.0k
53
votes
6
replies
9.7k
views
8 follow
Tool: list of dockerized bioinformatics apps
docker
updated 2.2 years ago by 43k • written 9.5 years ago by ★ 3.6k
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
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 6.7 years ago by ▴ 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 ▴ 50 • written 7.4 years ago by ★ 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 43k • written 8.1 years ago by ▴ 140
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
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 43k • written 3.4 years ago by ▴ 90
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
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 43k • written 11.1 years ago by 33k
32
votes
6
replies
12k
views
Tool: FASTA and FASTQ tools
Cpp FASTA Python FASTQ
updated 15 months ago by 43k • written 8.9 years ago by ★ 2.3k
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
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
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
29
votes
20
replies
3.6k
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
29
votes
29
replies
3.5k
views
6 follow
Tool: weld (former brew) - yet another fastq utility
illlumina python
updated 21 months ago by 43k • written 8.2 years ago by ▴ 40
28
votes
7
replies
11k
views
Tool: Quast Is A Convenient Tool For Assembly Evaluation
assembly quality
updated 10 months ago by 43k • written 11.2 years ago by ★ 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 43k • written 5.2 years ago by 87k
28
votes
4
replies
15k
views
Tool: Plotting GSEA output in R
RNA-Seq javaGSEA GSEA
updated 10 months ago by 43k • written 7.7 years ago by ▴ 850
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 ▴ 700 • written 23 months ago by ▴ 450
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 9.8 years ago by 19k
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 7.7 years ago by 47k
27
votes
6
replies
16k
views
Tool: Bioawk - Fasta, Fastq, Sam, Bed, Gff Aware Awk Programming
awk
updated 10 months ago by 43k • written 11.8 years ago by 100k
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
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 43k • written 7.9 years ago by ▴ 880
26
votes
4
replies
5.3k
views
Tool: Dgidb - Mining The Druggable Genome
dgidb drug-gene-interaction
updated 10 months ago by 43k • written 10.5 years ago by 20k
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
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 43k • written 9.3 years ago by ▴ 350
25
votes
19
replies
8.1k
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
25
votes
3
replies
4.9k
views
Tool: Quick statistics from the command line
statistics C
updated 16 months ago by 43k • written 8.8 years ago by ★ 2.3k
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
23
votes
19
replies
4.2k
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
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
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
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
22
votes
22
replies
18k
views
Tool: Pan-Cancer Analysis And Networks Of LncRNAs, MiRNAs, circRNAs, CeRNAs And RNA-Binding Proteins From TCGA 32 Cancer Types and CLIP-seq data
cancer TCGA RNA-Binding-Proteins miRNA lncRNA
updated 19 months ago by 43k • written 10.2 years ago by ▴ 860
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
733 results • Page 1 of 15
Recent Votes
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
Comment: To get p-values for the TPM
A: Where To Download Pam50 Gene Set?
A: Where To Download Pam50 Gene Set?
Answer: Fail to install umap-learn in R
Answer: Fail to install umap-learn in R
Recent Locations • All
United States, 1 minute ago
United States, 2 minutes ago
Portugal, 2 minutes ago
Cambridge, MA, 2 minutes ago
Kansas City, 3 minutes ago
United States, 4 minutes ago
United States, 5 minutes ago
Recent Awards • All
Popular Question to Russ ▴ 500
Popular Question to camillab. ▴ 160
Popular Question to pramach1 ▴ 40
Popular Question to Adyasha • 0
Popular Question to sehriban.buyukkilic ▴ 10
Popular Question to O.rka ▴ 710
Popular Question to Akash D ▴ 40
Recent Replies
Comment: PCA plot (Suggestions Needed) by Mensur Dlakic ★ 27k
Everything that @f1f58aed said, plus that there may be no data manipulation that will give you the clusters you expected. Sometimes there a…
Answer: Creating Synthetic Sequences for a ML Model by Mensur Dlakic ★ 27k
It is a good idea, though I don't see how it would work in practice. I think you will encounter at least additional problem on top of da…
Answer: PCA plot (Suggestions Needed) by Jeremy ▴ 890
Right now, the WT samples are clustering together, but you have one mutant sample off by itself, which could be an outlier. How did you sc…
Comment: Adding CB tag to bam file by GenoMax 141k
@yokofakun had written this: https://www.biostars.org/p/336965/ https://github.com/ruqianl/appendCB may also be useful.
Comment: Troubleshooting RNA-seq data with DNA contamination by GenoMax 141k
Please post information about your tool as a `tools` category post. Don't wait/ask other users to ask you.
Comment: Adding CB tag to bam file by Maria • 0
Sorry for the delay in my answer, I got sidetracked. I am using ```samtools addreplacerg -r "@RG\tID:$cell" -o $cell.bam -h $LINE``` bu…
Answer: Troubleshooting RNA-seq data with DNA contamination by haibol2017 ▴ 10
We just developed a R package to tackle this problem. Do you have stranded or unstranded RNA-seq data contaminated with gDNA? If you wou…
Comment: How to trim transcripts using information from NCBI contamination screen report by GenoMax 141k
`bbduk.sh` can use the transcripts as input. There is a `adapters.fa` included in the `resources` directory of the distribution. You can do…
Comment: PCA plot (Suggestions Needed) by swbarnes2 14k
Cross posted here (including the code used to make up the counts): https://support.bioconductor.org/p/9157911/#9157959
Comment: To get p-values for the TPM by swbarnes2 14k
RSEM returns a kind of p-value if you run it with the "prior-enhanced" option. Did you do that? Are you completely sure that's the value y…
Comment: How to trim transcripts using information from NCBI contamination screen report by Lada ▴ 30
i checked both of these programs (`bbduk` and `fastp`) and it seems they use reads as inputs (fastq formats)... how can I trim my transcrip…
Comment: AGeNT LocatIt by barslmn ★ 2.1k
He is already giving 32G, 320G for marking duplicates for exome is excessive. Is there a specific reason for using the tool?
Comment: How to convert plink files to Hapmap Format by bk11 ★ 2.3k
This looks good. Please try with using `--allow-no-sex flag` plink --bfile your_data_phenoUP --assoc --allow-no-sex --out your_data_ph…
Comment: How to convert plink files to Hapmap Format by Sofia • 0
SC899359_PC75420_A05 SC899359_PC75420_A05 0 0 0 2 SC899360_PC75415_D01 SC899360_PC75415_D01 0 0 0 2 SC899361_PC75425_H05 SC899361_PC75425_H…
Comment: How to convert plink files to Hapmap Format by bk11 ★ 2.3k
Please show me a few lines of phenotype updated .fam file. You can do `head your_data_phenoUP.fam` and paste result here. Please do not us…
Traffic: 2563 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6