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515 results • Page
2 of 11
Sort: Votes
Rank
Views
Votes
Replies
17
votes
9
replies
17k
views
6 follow
Tool:
ggrepel: repel overlapping text labels in ggplot2
R
visualization
updated 11 months ago by
Ram
43k • written 8.4 years ago by
Kamil
★ 2.3k
17
votes
9
replies
6.1k
views
Tool:
Pathomx: Metabolic Pathway Visualisation And Analysis
python
pathway-visualization
updated 10 months ago by
Ram
43k • written 11.1 years ago by
Martin Fitzpatrick
▴ 180
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
Ram
43k • written 10.3 years ago by
Matt Shirley
10k
16
votes
16
replies
7.7k
views
6 follow
Tool:
Oncofuse: Prediction Of Driver Gene Fusions From Ngs Data
annotation
fusion
rna-seq
ngs
updated 10 months ago by
Ram
43k • written 10.7 years ago by
mikhail.shugay
3.5k
16
votes
3
replies
11k
views
Tool:
Vcflib Documentation
vcf
updated 11 months ago by
Ram
43k • written 11.2 years ago by
Erik Garrison
★ 2.4k
15
votes
6
replies
7.2k
views
Tool:
Sambamba: High Performance Alternative For Samtools And Picard For Indexing, Sorting And Merging Bam Files
sambamba
bam
samtools
updated 10 months ago by
Ram
43k • written 10.6 years ago by
William
★ 5.3k
15
votes
9
replies
3.4k
views
Tool:
FlexiDot: highly customizable, ambiguity-aware dotplots
dotplot
visualization
sequence-analysis
updated 11 months ago by
Ram
43k • written 6.0 years ago by
toheitka
▴ 230
15
votes
19
replies
8.8k
views
6 follow
Tool:
Gemini: Integrative Exploration Of Genetic Variation And Genome Annotations
vcf
database
genome
variation
updated 11 months ago by
Ram
43k • written 11.1 years ago by
Aaronquinlan
12k
15
votes
2
replies
3.1k
views
Tool:
EnhancedVolcano becomes a pseudo-EnhancedMA
enhancedMA
enhancedvolcano
updated 11 months ago by
Ram
43k • written 3.7 years ago by
Kevin Blighe
88k
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 11 months ago by
Ram
43k • written 6.3 years ago by
uhrigs
▴ 150
14
votes
4
replies
4.8k
views
Tool:
Revolution (?) in CNA detection using exome/targeted sequencing
copy-number-alteration
next-gen
updated 10 months ago by
Ram
43k • written 9.1 years ago by
Irsan
★ 7.8k
14
votes
10
replies
7.9k
views
Tool:
ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization
ReactomePA
R
Visualization
Pathway
Bioconductor
updated 10 months ago by
Ram
43k • written 7.9 years ago by
Guangchuang Yu
★ 2.6k
14
votes
4
replies
4.5k
views
Tool:
Seq_File: C Library For Reading Multiple Bioinformatics Sequence File Formats
fasta
fastq
bam
sam
updated 10 months ago by
Ram
43k • written 11.4 years ago by
Jeremy Leipzig
22k
14
votes
3
replies
4.1k
views
Tool:
Bedops V2.2 Released
bed
updated 10 months ago by
Ram
43k • written 11.1 years ago by
Alex Reynolds
35k
13
votes
6
replies
4.9k
views
Tool:
GAWN - Genome Annotation Without Nightmares
genome-annotation
updated 11 months ago by
Ram
43k • written 6.8 years ago by
Eric Normandeau
11k
13
votes
1
reply
3.7k
views
Tool:
Script to compute the effective genome size: epic-effective
ChIP-Seq
updated 10 months ago by
Ram
43k • written 8.1 years ago by
endrebak
▴ 960
13
votes
1
reply
6.6k
views
Tool:
clusterProfiler: an R package for comparing biological themes among gene clusters
GO
clusterProfiler
KEGG
R
GSEA
updated 11 months ago by
Ram
43k • written 7.9 years ago by
Guangchuang Yu
★ 2.6k
13
votes
2
replies
7.4k
views
Tool:
Software For Detecting Differential Abundance In Meta-Genomic Samples
metagenomics
updated 10 months ago by
Ram
43k • written 11.6 years ago by
Istvan Albert
100k
13
votes
4
replies
2.1k
views
Tool:
iProtein.info website: Express online visualization of human genome pathways
reactome
signalling
visualization
pathway
updated 11 months ago by
Ram
43k • written 6.4 years ago by
serena_yu
▴ 110
13
votes
14
replies
6.2k
views
9 follow
Tool:
open-cravat: variant annotation tool
open-cravat
updated 11 months ago by
Ram
43k • written 5.4 years ago by
slcrick
▴ 260
13
votes
8
replies
4.3k
views
Tool:
MSigDB for Multiple Organisms in a Tidy Data Format
msigdb
pathways
R
gsea
updated 11 months ago by
Ram
43k • written 6.1 years ago by
igor
13k
13
votes
0
replies
2.9k
views
Tool:
Book: GNU Parallel 2018 - for beginners and advanced users
parallel
ngs
updated 11 months ago by
Ram
43k • written 5.6 years ago by
ole.tange
★ 4.4k
13
votes
7
replies
9.8k
views
Tool:
Command-Line Software For Bigwig Data
bigwig
updated 11 months ago by
Ram
43k • written 10.5 years ago by
andypohl
▴ 90
13
votes
6
replies
5.2k
views
Tool:
csvtk - a cross-platform, efficient, practical and pretty CSV/TSV toolkit
CSV
Golang
TSV
9 months ago by
shenwei356
8.5k
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
Ram
43k • written 10.8 years ago by
mikhail.shugay
3.5k
13
votes
14
replies
2.3k
views
Tool:
Collaboration on an empirical QC tool
RNA-Seq
QC
sequencing
updated 10 months ago by
Ram
43k • written 7.0 years ago by
Michael
54k
12
votes
0
replies
4.8k
views
Tool:
UMI-Tools 0.5, now with tools for cell barcoded scRNA-seq
UMI
RNA-Seq
single-cell
updated 11 months ago by
Ram
43k • written 6.7 years ago by
i.sudbery
19k
12
votes
1
reply
2.7k
views
Tool:
iStack: an R solution for plotting stacked bars using custom icons
R
updated 11 months ago by
Ram
43k • written 5.4 years ago by
brettgao2018
▴ 150
12
votes
6
replies
3.5k
views
Tool:
Variant annotation and filtration server ALAPY Genome Explorer (AGx)
vcf
variant-annotation
variant-interpretation
updated 10 months ago by
Ram
43k • written 7.0 years ago by
Petr Ponomarenko
★ 2.8k
12
votes
3
replies
2.8k
views
Tool:
Hiplot: a simple and user-friendly visualization platform for scientific data
R
microbial
RNA-Seq
visualization
updated 11 months ago by
Ram
43k • written 3.8 years ago by
Hiplot
▴ 130
12
votes
3
replies
3.1k
views
Tool:
The Biopieces Are A Collection Of Bioinformatics Tools
sequence
updated 10 months ago by
Ram
43k • written 11.3 years ago by
Medhat
9.7k
12
votes
9
replies
7.8k
views
Tool:
gogadget: an R package for go analysis visualization and interpretation
goseq
R
RNA-Seq
gogadget
updated 11 months ago by
Ram
43k • written 7.8 years ago by
Benn
8.3k
12
votes
4
replies
1.1k
views
Tool:
BBTools 39.03 released!
BBTools
BBMap
7 months ago by
Brian Bushnell
20k
12
votes
5
replies
6.2k
views
Tool:
AGAT - Another Gff/Gtf Analysis Toolkit
gff
gtf
updated 10 months ago by
Ram
43k • written 4.4 years ago by
Juke34
8.6k
12
votes
7
replies
3.2k
views
Tool:
Chromozoom: The Genome Browser That Lets You Fly!
genome-browser
browser
updated 10 months ago by
Ram
43k • written 11.2 years ago by
Istvan Albert
100k
11
votes
2
replies
5.3k
views
Tool:
ChIPQC: a package for assessing quality of ChIP-seq samples and experiments
quality-control
quality-assessment
ChIP-Seq
updated 10 months ago by
Ram
43k • written 10.1 years ago by
Rory Stark
★ 2.0k
11
votes
2
replies
7.1k
views
Tool:
fastp (the ultra-fast all-in-one FASTQ preprocessing tool) v0.18.0 released, 2X faster, with many new features.
fastp
QC
updated 11 months ago by
Ram
43k • written 5.9 years ago by
chen
★ 2.5k
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 11 months ago by
Ram
43k • written 5.8 years ago by
btsui
▴ 300
11
votes
3
replies
2.8k
views
Tool:
Sequence Database curator
sequence
fastq
sequencing
blast
updated 11 months ago by
Ram
43k • written 7.3 years ago by
Eslam Samir
▴ 110
11
votes
5
replies
2.6k
views
Tool:
A resource with diverse databases and tools for SARS-CoV-2 (COVID-19) bioinformatics -- Updates
SARS-CoV-2
Corona
Databases
COVID-19
updated 11 months ago by
Ram
43k • written 4.2 years ago by
Michael
▴ 270
11
votes
0
replies
3.0k
views
Tool:
Pyblue: A Simple Tool To Generate Data/Code Oriented Static Web Sites (version 2.0 released)
pyblue
updated 10 months ago by
Ram
43k • written 10.8 years ago by
Istvan Albert
100k
11
votes
1
reply
4.8k
views
Tool:
Ideogram.js: a JavaScript library for chromosome visualization
javascript
chromosome
visualization
ideogram
updated 11 months ago by
Ram
43k • written 6.2 years ago by
Eric Weitz
▴ 120
11
votes
2
replies
13k
views
Tool:
Multiplex PCR Primer Design Tools
multiplex-PCR
updated 11 months ago by
Ram
43k • written 6.7 years ago by
Shicheng Guo
★ 9.4k
11
votes
3
replies
4.6k
views
Tool:
Dgidb - Mining The Druggable Genome
dgidb
drug-gene-interaction
updated 10 months ago by
Ram
43k • written 10.6 years ago by
Obi Griffith
20k
11
votes
2
replies
781
views
Tool:
Pipeline Generator
gpt
updated 9 months ago by
LauferVA
4.2k • written 9 months ago by
Sasha
▴ 850
10
votes
0
replies
5.8k
views
Tool:
Shell utilities for QC of FASTQ/FASTA files (based on perl one-liners)
PERL
GNUPLOT
FASTA
FASTQ
FastQC
updated 10 months ago by
Ram
43k • written 10.1 years ago by
umer.zeeshan.ijaz
★ 1.8k
10
votes
2
replies
2.1k
views
Tool:
Onezoom For Viewing Large Phylogenetic Tree Data
phylogeny
updated 10 months ago by
Ram
43k • written 11.6 years ago by
Mary
11k
10
votes
12
replies
1.9k
views
Tool:
PanDepth, an ultra-fast and efficient genomic tool for coverage calculation
bam
paf
depth
cram
coverage
3 months ago by
Huiyang
▴ 190
10
votes
1
reply
7.5k
views
Tool:
Comb-P: Combining Spatially Correlated P-Values
methylation
updated 10 months ago by
Ram
43k • written 11.6 years ago by
brentp
24k
10
votes
5
replies
2.5k
views
Tool:
Genozip: A new compression tool for FASTQ, BAM, VCF and more
bam
vcf
fastq
compression
10 months ago by
Divon
▴ 230
515 results • Page
2 of 11
Recent Votes
A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
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Recent Replies
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors)
by
nguyenn6
• 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed
by
anton.i.petrov
• 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp
by
analyst
▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R
by
1769mkc
★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks
by
ATpoint
82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
by
Joe
21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
Gordon Smyth
★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF)
by
aidangcruickshank
▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data?
by
Ngrin
• 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2
by
swbarnes2
14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
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