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
518 results • Page
2 of 11
Sort: replies
Rank
Views
Votes
Replies
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
Ram
43k • written 6.5 years ago by
chen
★ 2.5k
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 10 months ago by
Ram
43k • written 6.2 years ago by
uhrigs
▴ 150
7
votes
11
replies
3.2k
views
Tool:
Graphical User Interface for creating an automated RNA-Sequencing Pipeline via Kallisto and DESeq2
DESeq2
kallisto
RNA-Seq
updated 10 months ago by
Ram
43k • written 5.3 years ago by
Anthony.Knox
▴ 60
21
votes
11
replies
11k
views
Tool:
Segemehl: A Fast One-Stop-Shop Mapping Tool
mapping
next-gen
updated 10 months ago by
Ram
43k • written 11.6 years ago by
David Langenberger
11k
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 10.2 years ago by
Matt Shirley
10k
7
votes
10
replies
1.5k
views
Tool:
SamReadViewer - A small utility to visualise read alignment directly from sam format without reference.
samreadviewer
updated 10 months ago by
Ram
43k • written 3.6 years ago by
Juke34
8.6k
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 7.8 years ago by
Guangchuang Yu
★ 2.6k
3
votes
10
replies
1.7k
views
Tool:
Quick & dirty DNA coordinates in any mac app
sequence
alignment
updated 10 months ago by
Ram
43k • written 6.2 years ago by
rleach
▴ 180
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 10 months ago by
Ram
43k • written 5.8 years ago by
btsui
▴ 300
23
votes
10
replies
12k
views
Tool:
ggtree: phylogenetic tree visualization and annotation
ggtree
phylogeny
visualization
updated 10 months ago by
Ram
43k • written 7.9 years ago by
Guangchuang Yu
★ 2.6k
7
votes
9
replies
4.0k
views
Tool:
VCF-simplify: a VCF simplification tool.
VCF
variants
genome
updated 10 months ago by
Ram
43k • written 6.1 years ago by
kirannbishwa01
★ 1.6k
15
votes
9
replies
3.4k
views
Tool:
FlexiDot: highly customizable, ambiguity-aware dotplots
dotplot
visualization
sequence-analysis
updated 10 months ago by
Ram
43k • written 6.0 years ago by
toheitka
▴ 230
12
votes
9
replies
7.8k
views
Tool:
gogadget: an R package for go analysis visualization and interpretation
goseq
R
RNA-Seq
gogadget
updated 10 months ago by
Ram
43k • written 7.8 years ago by
Benn
8.3k
19
votes
9
replies
6.1k
views
Tool:
Rlsim, A Package For Simulating Rna-Seq Library Preparation With Parameter Estimation
simulation
rna-seq
pcr
illumina
updated 11 months ago by
Ram
43k • written 11.1 years ago by
Botond Sipos
★ 1.7k
3
votes
9
replies
3.6k
views
Tool:
Download all refseq/genbank bacterial genomes from NCBI
genome
sequencing
updated 10 months ago by
Ram
43k • written 7.3 years ago by
johnsrc06
▴ 10
8
votes
9
replies
8.9k
views
Tool:
Lofreq: A Fast And Sensitive Variant-Caller For Inferring Single-Nucleotide Variants From Ngs Data
snp
next-gen
somatic-variant
updated 10 months ago by
Ram
43k • written 11.6 years ago by
Andreas
★ 2.5k
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
9
votes
9
replies
4.6k
views
Tool:
pyCirclize - Circular visualization in Python
visualization
circos
matplotlib
genome
python
updated 9 months ago by
shuo
• 0 • written 17 months ago by
moshi
▴ 150
4
votes
9
replies
2.7k
views
Tool:
CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.3 years ago by
dvelmeshev
• 0
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
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 8.3 years ago by
Kamil
★ 2.3k
22
votes
8
replies
6.6k
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
5
votes
8
replies
7.0k
views
6 follow
Tool:
Converting MUMmer snps file to a real VCF file
VCF
mummer
SNP
updated 10 months ago by
Ram
43k • written 4.7 years ago by
Matteo Schiavinato
★ 3.6k
3
votes
8
replies
6.3k
views
Tool:
MFEprimer-2.0: A Fast Thermodynamics-Based Program For Checking Pcr Primer Specificity
primer
pcr
updated 10 months ago by
Ram
43k • written 11.9 years ago by
Wubin Qu
▴ 170
10
votes
8
replies
1.9k
views
6 follow
Tool:
"bioalcidae, samjs and vcffilterjs" published in bioinformatics.
jvarkit
bam
vcf
javascript
java
updated 10 months ago by
Ram
43k • written 6.5 years ago by
Pierre Lindenbaum
161k
2
votes
8
replies
3.7k
views
Tool:
Mirnakey - A Software Pipeline For The Analysis Of Microrna Deep Sequencing Data
mirna
updated 10 months ago by
Ram
43k • written 11.7 years ago by
Istvan Albert
100k
3
votes
8
replies
727
views
Tool:
Generate unit-tested, ready-to-run pipelines using natural language prompting
NGS
pipeline
genomics
cloud
AI
updated 3 months ago by
Ram
43k • written 3 months ago by
Kevin
▴ 50
6
votes
8
replies
4.9k
views
Tool:
Read-based phasing with WhatsHap
phasing
updated 10 months ago by
Ram
43k • written 7.4 years ago by
Marcel M
▴ 100
13
votes
8
replies
4.3k
views
Tool:
MSigDB for Multiple Organisms in a Tidy Data Format
msigdb
pathways
R
gsea
updated 10 months ago by
Ram
43k • written 6.1 years ago by
igor
13k
7
votes
7
replies
4.7k
views
Tool:
Variant Annotation, Analysis and Search Tool - VAAST2
VAAST2
VAAST
updated 10 months ago by
Ram
43k • written 10.0 years ago by
Zev.Kronenberg
12k
9
votes
7
replies
3.5k
views
Tool:
metaViC: Virus metagenomics pipeline for unknown host or in absence of a host genome
Assembly
metagenomics
ngs
updated 10 months ago by
Ram
43k • written 7.7 years ago by
Sej Modha
5.3k
6
votes
7
replies
2.5k
views
Tool:
Workflow for structural variants from long read sequencing data
structural-variation
pacbio
nanopore
snakemake
updated 10 months ago by
Ram
43k • written 5.6 years ago by
WouterDeCoster
47k
3
votes
7
replies
1.4k
views
Tool:
New method for protein secondary structure prediction
protein
secondary-structure
updated 10 months ago by
Ram
43k • written 4.7 years ago by
vytarasov
▴ 180
9
votes
7
replies
3.0k
views
Tool:
DiffBind 3.0: Extensive updates in Bioconductor 3.12
DiffBind
ChIP-Seq
diffbind
ATAC-seq
chipseq
updated 11 months ago by
Ram
43k • written 3.5 years ago by
Rory Stark
★ 2.0k
6
votes
7
replies
3.1k
views
Tool:
MutScan: detect and visualize target mutations by just scanning FastQ, 50X faster than normal pipelines
Mutation
FastQ
MutScan
OpenGene
updated 10 months ago by
Ram
43k • written 7.1 years ago by
chen
★ 2.5k
2
votes
7
replies
2.7k
views
Tool:
metaflagstat.py - painless bam/sam read flag counting
samtools
bam
updated 10 months ago by
Ram
43k • written 9.7 years ago by
John
13k
2
votes
7
replies
2.9k
views
Tool:
An online cute tool to query tumor-gene data from MSK-IMPACT project
MSK-IMPACT
tumor
mutation
MSK
updated 10 months ago by
Ram
43k • written 7.0 years ago by
chen
★ 2.5k
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
4
votes
7
replies
4.6k
views
6 follow
Tool:
MAGERI: a software tool for calling rare variants and detecting circulating tumor DNA from UMI-tagged high-throughput sequencing data
rare-variant
resequencing
umi
ctDNA
updated 3 months ago by
blid11
• 0 • written 7.0 years ago by
mikhail.shugay
3.5k
5
votes
7
replies
3.7k
views
Tool:
CircTools: Softwares for Discovering circRNA-microRNA Interactions from CLIP-Seq Datasets
circRNA
CLIP-seq
microRNA
RNA-seq
Interactome
updated 10 months ago by
Ram
43k • written 6.0 years ago by
lsp03yjh
▴ 860
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 11.0 years ago by
chbelhumeur2000
▴ 40
4
votes
7
replies
1.4k
views
Tool:
Elloreas, a new genome assembler
Assembly
next-gen
updated 10 months ago by
Ram
43k • written 3.9 years ago by
shelkmike
★ 1.2k
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
13
votes
7
replies
9.8k
views
Tool:
Command-Line Software For Bigwig Data
bigwig
updated 10 months ago by
Ram
43k • written 10.5 years ago by
andypohl
▴ 90
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 11.9 years ago by
Istvan Albert
100k
8
votes
6
replies
5.8k
views
Tool:
chromoMap- R package for Interactive visualization and Annotation of chromosomes or regions of any living organism.
annotation
R
genome
visualization
updated 11 months ago by
Ram
43k • written 5.1 years ago by
lakshayanand15
▴ 80
13
votes
6
replies
4.9k
views
Tool:
GAWN - Genome Annotation Without Nightmares
genome-annotation
updated 10 months ago by
Ram
43k • written 6.8 years ago by
Eric Normandeau
11k
0
votes
6
replies
1.5k
views
Tool:
Script: Downloading fastq files from ENA database
next-gen-sequencing
RNA-Seq
updated 10 months ago by
Ram
43k • written 3.3 years ago by
jayeshkumarsundaram
• 0
7
votes
6
replies
5.1k
views
Tool:
mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
depth-of-coverage
exome
WGS
updated 10 months ago by
Ram
43k • written 6.3 years ago by
brentp
24k
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
518 results • Page
2 of 11
Recent Votes
Answer: How to compute TPM normalized values for TCGA miRNA data?
C: Convert .Txt File To Bed File
A: Get nonoverlapping regions of two bed files
Get nonoverlapping regions of two bed files
Answer: install package
Answer: How I do lift over a Plink bim file from Hg18 to Hg19.
Answer: joint callset and vcf sorting, unknown TAG issue
Recent Locations •
All
Russia,
just now
China,
just now
United States,
1 minute ago
Australia,
2 minutes ago
China,
6 minutes ago
Australia,
7 minutes ago
China,
7 minutes ago
Recent Awards •
All
Popular Question
to
rj.rezwan
• 0
Scholar
to
colindaven
6.4k
Scholar
to
pjb39
▴ 200
Popular Question
to
Jen
▴ 70
Scholar
to
Pierre Lindenbaum
161k
Popular Question
to
Michael
54k
Popular Question
to
Kai_Qi
▴ 130
Recent Replies
Comment: How to convert normalized BigWig file to count matrix?
by
feather-W
• 0
Hi ATpoint, Thanks for your reply!
Comment: How to convert normalized BigWig file to count matrix?
by
feather-W
• 0
Hi Pierre, Thanks for your reply! I want to get a feature count matrix from coverage data stored in BigWig files. And this BigWig file ha…
Comment: Extracting mutation status from MAF files - TCGA
by
Zhenyu Zhang
★ 1.2k
you can assume all genes without mutation is WT (easy) while controlling for (difficult) - coverage - capture region - germline - the …
Comment: Obtaining Infinium Methylation450K manifest for hg38
by
Zhenyu Zhang
★ 1.2k
Since you are getting data from the GDC, analysis-related reference/annotations can be found in the GDC reference page here https://gdc.can…
Comment: Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in py
by
fracarb8
★ 1.6k
I saw that, but considering that your analysis is in seurat and that both liana and liana+ are from the same developers, it might be quicke…
Answer: Nomalization - TCGA, RNA-seq and Microarray
by
Zhenyu Zhang
★ 1.2k
You can rank normalize them, but to tell the truth, I won't trust any conclusion you can draw from such combined data. The recommended …
Comment: How to remove multiple batch effects from RNA-seq data before limma differential
by
ATpoint
82k
Include confounders into the limma design. No need for upfront removal. Note that libsize is taken care of by normalizing usually. Are you …
Comment: Longest transcript variant per gene
by
sansan_96
▴ 90
Thank you very much, success in your projects.
Comment: In IGV is this a heterogeneous mutation or false call?
by
Tuck898
• 0
Thanks for the input :)
Comment: install package: package ‘gmwm’ is not available for this version of R
by
Pine
▴ 20
This seems to indicate that the package itself (or packages it depends on) are not compatible with the R version you are using. Next step c…
Answer: Tissue-specific DEG analysis with DEseq2
by
arctic
▴ 40
Not my area of expertise but GTEx portal seems to offer visual comparison of expression across tissues, maybe checking their pipeline could…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
> I think I am mostly struggling with what would need to be coded to my dataset here and how to run this loop on my set in general. i do…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
ajbarrett98
• 0
Pierre, I am a novice at all of this in general and I have never used Java-based programming before. I may not be able to properly wrangl…
Answer: Practical Haplotype Graph v2 not finding correct paths
by
pjb39
▴ 200
There have been a couple of bugs found that affect imputation accuracy, one in build-kmer-index and one in find-paths. The find-paths bug o…
Comment: Output file of satools flagstat empty
by
Mathew
▴ 100
Hi, In your samtools flagstat, -o specifies the output format. This can be set to 'default', 'json', or 'tsv'. If -o is not specified , t…
Traffic: 1443 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