Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this year
all time
today
this week
this month
this year
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
44k • written 8.4 years ago by
Kamil
★ 2.3k
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 11 months ago by
Ram
44k • 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 11 months ago by
Ram
44k • 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
44k • written 11.2 years ago by
Erik Garrison
★ 2.4k
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
44k • written 6.3 years ago by
uhrigs
▴ 150
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
44k • written 11.1 years ago by
Aaronquinlan
12k
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 11 months ago by
Ram
44k • written 10.7 years ago by
William
★ 5.3k
15
votes
2
replies
3.1k
views
Tool:
EnhancedVolcano becomes a pseudo-EnhancedMA
enhancedMA
enhancedvolcano
updated 11 months ago by
Ram
44k • written 3.7 years ago by
Kevin Blighe
88k
15
votes
9
replies
3.4k
views
Tool:
FlexiDot: highly customizable, ambiguity-aware dotplots
dotplot
visualization
sequence-analysis
updated 11 months ago by
Ram
44k • written 6.0 years ago by
toheitka
▴ 230
14
votes
4
replies
4.8k
views
Tool:
Revolution (?) in CNA detection using exome/targeted sequencing
copy-number-alteration
next-gen
updated 11 months ago by
Ram
44k • written 9.1 years ago by
Irsan
★ 7.8k
14
votes
4
replies
4.5k
views
Tool:
Seq_File: C Library For Reading Multiple Bioinformatics Sequence File Formats
fasta
fastq
bam
sam
updated 11 months ago by
Ram
44k • written 11.4 years ago by
Jeremy Leipzig
22k
14
votes
3
replies
4.1k
views
Tool:
Bedops V2.2 Released
bed
updated 11 months ago by
Ram
44k • written 11.1 years ago by
Alex Reynolds
35k
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 11 months ago by
Ram
44k • written 7.9 years ago by
Guangchuang Yu
★ 2.6k
13
votes
7
replies
9.8k
views
Tool:
Command-Line Software For Bigwig Data
bigwig
updated 11 months ago by
Ram
44k • written 10.6 years ago by
andypohl
▴ 90
13
votes
1
reply
3.7k
views
Tool:
Script to compute the effective genome size: epic-effective
ChIP-Seq
updated 11 months ago by
Ram
44k • written 8.1 years ago by
endrebak
▴ 960
13
votes
14
replies
2.3k
views
Tool:
Collaboration on an empirical QC tool
RNA-Seq
QC
sequencing
updated 11 months ago by
Ram
44k • written 7.0 years ago by
Michael
54k
13
votes
6
replies
4.9k
views
Tool:
GAWN - Genome Annotation Without Nightmares
genome-annotation
updated 11 months ago by
Ram
44k • written 6.8 years ago by
Eric Normandeau
11k
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
44k • written 7.9 years ago by
Guangchuang Yu
★ 2.6k
13
votes
14
replies
6.2k
views
9 follow
Tool:
open-cravat: variant annotation tool
open-cravat
updated 11 months ago by
Ram
44k • written 5.4 years ago by
slcrick
▴ 260
13
votes
2
replies
7.4k
views
Tool:
Software For Detecting Differential Abundance In Meta-Genomic Samples
metagenomics
updated 11 months ago by
Ram
44k • 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
44k • written 6.4 years ago by
serena_yu
▴ 110
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 11 months ago by
Ram
44k • written 10.8 years ago by
mikhail.shugay
3.5k
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
44k • written 5.6 years ago by
ole.tange
★ 4.4k
13
votes
8
replies
4.4k
views
Tool:
MSigDB for Multiple Organisms in a Tidy Data Format
msigdb
pathways
R
gsea
updated 11 months ago by
Ram
44k • written 6.1 years ago by
igor
13k
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
44k • written 6.8 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
44k • written 5.5 years ago by
brettgao2018
▴ 150
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
44k • 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 11 months ago by
Ram
44k • written 11.3 years ago by
Medhat
9.7k
12
votes
4
replies
1.1k
views
Tool:
BBTools 39.03 released!
BBTools
BBMap
7 months ago by
Brian Bushnell
20k
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
44k • written 7.8 years ago by
Benn
8.3k
12
votes
5
replies
6.2k
views
Tool:
AGAT - Another Gff/Gtf Analysis Toolkit
gff
gtf
updated 11 months ago by
Ram
44k • 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 11 months ago by
Ram
44k • written 11.2 years ago by
Istvan Albert
100k
12
votes
6
replies
3.5k
views
Tool:
Variant annotation and filtration server ALAPY Genome Explorer (AGx)
vcf
variant-annotation
variant-interpretation
updated 11 months ago by
Ram
44k • written 7.0 years ago by
Petr Ponomarenko
★ 2.8k
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
44k • written 4.2 years ago by
Michael
▴ 270
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 11 months ago by
Ram
44k • 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
44k • written 5.9 years ago by
chen
★ 2.5k
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
44k • written 6.2 years ago by
Eric Weitz
▴ 120
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
44k • written 5.8 years ago by
btsui
▴ 300
11
votes
2
replies
786
views
Tool:
Pipeline Generator
gpt
updated 9 months ago by
LauferVA
4.2k • written 9 months ago by
Sasha
▴ 850
11
votes
2
replies
13k
views
Tool:
Multiplex PCR Primer Design Tools
multiplex-PCR
updated 11 months ago by
Ram
44k • written 6.8 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 11 months ago by
Ram
44k • written 10.6 years ago by
Obi Griffith
20k
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 11 months ago by
Ram
44k • written 10.8 years ago by
Istvan Albert
100k
11
votes
3
replies
2.8k
views
Tool:
Sequence Database curator
sequence
fastq
sequencing
blast
updated 11 months ago by
Ram
44k • written 7.3 years ago by
Eslam Samir
▴ 110
10
votes
1
reply
7.5k
views
Tool:
Comb-P: Combining Spatially Correlated P-Values
methylation
updated 11 months ago by
Ram
44k • written 11.6 years ago by
brentp
24k
10
votes
2
replies
2.1k
views
Tool:
Onezoom For Viewing Large Phylogenetic Tree Data
phylogeny
updated 11 months ago by
Ram
44k • written 11.6 years ago by
Mary
11k
10
votes
6
replies
5.7k
views
Tool:
Shell script to automate trimmomatic for multiple samples
bash
shell
trimmomatic
updated 11 months ago by
Ram
44k • written 5.0 years ago by
lakhujanivijay
5.8k
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
3
replies
6.3k
views
Tool:
GenVisR: Genomic Visualizations in R
visualization
genomic
RNA-Seq
genvisr
updated 11 months ago by
Ram
44k • written 7.9 years ago by
Obi Griffith
20k
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
Answer: Microbial community analysis pipelines in metagenomics
A: What are chimeric reads?
Answer: Allele count of 2 for homoplasmic MT variants in VCF
Find count of reads in BAM file that fall within BED region
Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
C: Reads mapped to another chromosome in paired-end data of RNA-seq
Recent Locations •
All
Berlin,
7 minutes ago
Australia,
10 minutes ago
United States,
13 minutes ago
United States,
15 minutes ago
EEUU,
16 minutes ago
Poland,
18 minutes ago
United States,
19 minutes ago
Recent Awards •
All
Scholar
to
LChart
3.9k
Scholar
to
ATpoint
82k
Popular Question
to
liyong
▴ 80
Popular Question
to
Shicheng Guo
★ 9.4k
Popular Question
to
reza
▴ 300
Popular Question
to
mhale
▴ 20
Teacher
to
Ashutosh Pandey
12k
Recent Replies
Comment: Mouse or Rat Gene Expression Data Similar to GTEx
by
GenoMax
142k
Past thread: https://www.biostars.org/p/178266/
Answer: Mouse or Rat Gene Expression Data Similar to GTEx
by
GenoMax
142k
Mouse bodymap samples : https://ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA375882%20&o=acc_s%3Aa
Answer: Mouse or Rat Gene Expression Data Similar to GTEx
by
bk11
★ 2.5k
Here is the [RatGTEx][1] [1]: https://ratgtex.org
Comment: Random Access remote BAM files
by
a.penatauber
• 0
Hi Lucas, I am looking for a similar functionality as I'm working with a large volume of CRAM files on S3, and downloading them whole would…
Comment: from CRAM to fastq
by
ATpoint
82k
Yes, but I still think that with this syntax you get an uncompressed file, because samtools does not detect the gz suffix. Just take a `hea…
Comment: merge overlaps and remove non overlap genomic windows
by
reza
▴ 300
Overlap of "Ch1 200 250" and "Ch1 150 220" is "Ch1 200 220", but I want to combine windows that have overlap. Thus, my goal is to combine …
Comment: Flag multiple filtering steps on VCF files using VEP
by
Pierre Lindenbaum
162k
I don't understand that question.
Comment: merge overlaps and remove non overlap genomic windows
by
Pierre Lindenbaum
162k
> But your answer is exactly the opposite of what I want oh I see. but i don't understand the logic why: "Ch1 200 250" and "Ch1 150 220" …
Comment: merge overlaps and remove non overlap genomic windows
by
reza
▴ 300
sorry i edited my example. But your answer is exactly the opposite of what I want
Answer: merge overlaps and remove non overlap genomic windows
by
Pierre Lindenbaum
162k
> have two bed files these are not bed files. A chromosome is missing in chromosome 1 > How can I create a file from the two mention…
Comment: Small secondary peak for per sequence GC content - FASTQC results (bulk RNA-seq)
by
GenoMax
142k
Have you checked for presence of rRNA in the affected samples? That can be one possibility for these peaks. In theory if you are aligning …
Comment: Allele count of 2 for homoplasmic MT variants in VCF
by
GenoMax
142k
Please accept the answer (green check mark) to provide closure to this thread.
Comment: Trimmomatic running but files containing purged reads are empty
by
GenoMax
142k
Perhaps there were no low quality reads either.
Comment: Allele count of 2 for homoplasmic MT variants in VCF
by
Arton
▴ 10
Thank you for the helpful answer!
Comment: How to get the ratio of allele counts from GATK derived VCF file?
by
DBScan
▴ 300
I think GATK only counts informative reads in AD, do you have a DP field? DP should be closer what FreeBayes reports. You can also check GA…
Traffic: 1668 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