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 : all time
all time
today
this week
this month
this year
737 results • Page
2 of 15
Sort: replies
Rank
Views
Votes
Replies
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
19
votes
14
replies
8.2k
views
7 follow
Tool:
AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
PolyG
Quality-Control
Filtering
Fastq
AfterQC
updated 11 months ago by
Ram
43k • written 8.0 years ago by
chen
★ 2.5k
4
votes
13
replies
2.8k
views
Tool:
SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
pathway-analysis
visualization
Pathview
SBGN
updated 11 months ago by
Ram
43k • written 3.2 years ago by
bigmawen
▴ 430
53
votes
13
replies
5.7k
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 16 months ago by
Ram
43k • written 9.0 years ago by
Daniel
★ 4.0k
0
votes
13
replies
2.6k
views
Tool:
HIT'nDRIVE: Network based cancer driver genes prioritization algorithm using Hitting Time
network
driver-gene
software
updated 11 months ago by
Ram
43k • written 6.8 years ago by
raunakms
★ 1.1k
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
54
votes
13
replies
10k
views
6 follow
Tool:
Bedtools: Analyzing Genomic Features
bedtools
updated 10 months ago by
Ram
43k • written 12.1 years ago by
Istvan Albert
100k
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
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 11 months ago by
Ram
43k • written 6.6 years ago by
chen
★ 2.5k
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 2.6 years ago by
Ram
43k • written 9.9 years ago by
Malachi Griffith
20k
11
votes
12
replies
4.9k
views
Tool:
Mapsembler2 targeted micro assembly and visualization of the local assembly graph
minia
mapsembler
next-gen
Assembly
updated 2.1 years ago by
Ram
43k • written 9.8 years ago by
pierre.peterlongo
▴ 900
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
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 11 months ago by
Ram
43k • written 5.4 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 11.7 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 10.3 years ago by
Matt Shirley
10k
21
votes
11
replies
2.8k
views
Tool:
log / log.bio - keeping track of command line workflows
ac.gt
log.bio
log
updated 20 months ago by
Ram
43k • written 8.7 years ago by
John
13k
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
23
votes
10
replies
12k
views
Tool:
ggtree: phylogenetic tree visualization and annotation
ggtree
phylogeny
visualization
updated 11 months ago by
Ram
43k • written 7.9 years ago by
Guangchuang Yu
★ 2.6k
7
votes
10
replies
1.5k
views
Tool:
SamReadViewer - A small utility to visualise read alignment directly from sam format without reference.
samreadviewer
updated 11 months ago by
Ram
43k • written 3.6 years ago by
Juke34
8.6k
5
votes
10
replies
2.5k
views
Tool:
Tools Section Now Enabled
meta
biostars
updated 15 months ago by
Ram
43k • written 12.1 years ago by
Istvan Albert
100k
3
votes
10
replies
1.7k
views
Tool:
Quick & dirty DNA coordinates in any mac app
sequence
alignment
updated 11 months ago by
Ram
43k • written 6.2 years ago by
rleach
▴ 180
6
votes
10
replies
4.6k
views
Tool:
Giant Virus Finder - discover giant virus sequences in metagenomes
Giant-Virus-Finder
updated 14 months ago by
Ram
43k • written 8.2 years ago by
Csaba Kerepesi
▴ 350
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
8
votes
10
replies
7.2k
views
7 follow
Tool:
Transcription Factor Binding Sites, Motifs and Expression Profiles from ~10200 ChIP-seq and ~20000 RNA-seq samples
ChIP-Seq
transcription-factor
miRNA
lncRNA
updated 13 months ago by
Ram
43k • written 7.6 years ago by
lsp03yjh
▴ 860
6
votes
10
replies
4.4k
views
Tool:
Wham - a structural variant caller and association testing framework
genotype
gwas
bwa-mem
bam
structural-variant
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
Zev.Kronenberg
12k
7
votes
9
replies
4.0k
views
Tool:
VCF-simplify: a VCF simplification tool.
VCF
variants
genome
updated 11 months ago by
Ram
43k • written 6.1 years ago by
kirannbishwa01
★ 1.6k
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
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
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
46
votes
9
replies
43k
views
7 follow
Tool:
Tools to merge overlapping paired-end reads
ngs
Assembly
fastq
updated 13 months ago by
Charles-Alexandre Roy
▴ 50 • written 7.5 years ago by
Abdul Rafay Khan
★ 1.2k
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
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
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
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
16
votes
9
replies
8.7k
views
Tool:
Introducing eLabFTW : free open source electronic lab notebook
eln
open-source
notebook-software
updated 2.4 years ago by
Ram
43k • written 9.7 years ago by
Nico
▴ 190
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
8
votes
9
replies
9.0k
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
9
votes
9
replies
4.7k
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
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 11 months ago by
Ram
43k • written 5.6 years ago by
sonpham
▴ 580
3
votes
8
replies
740
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
8
votes
8
replies
2.9k
views
Tool:
DiscoSnp++ 2.1.2 release: now genotypes and creates VCFs
SNP
discosnp
genotyping
indel
updated 23 months ago by
Ram
43k • written 9.2 years ago by
pierre.peterlongo
▴ 900
5
votes
8
replies
7.1k
views
6 follow
Tool:
Converting MUMmer snps file to a real VCF file
VCF
mummer
SNP
updated 11 months ago by
Ram
43k • written 4.7 years ago by
Matteo Schiavinato
★ 3.6k
15
votes
8
replies
2.4k
views
Tool:
One Stop Solution for NGS Data Analysis
Predefined Robust NGS Analysis Tool
8.1 years ago by
Persistent LABS
▴ 750
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
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
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 12.0 years ago by
Wubin Qu
▴ 170
12
votes
8
replies
3.2k
views
Tool:
BioBit: Global bioinformatics chat
communication
updated 13 months ago by
Ram
43k • written 7.9 years ago by
vadim.nazarov
▴ 90
9
votes
8
replies
3.8k
views
6 follow
Tool:
NCBI-SRA File Downloader
NCBI
sra
sequence
updated 14 months ago by
Ram
43k • written 8.7 years ago by
sanjay.deshpande
▴ 50
8
votes
8
replies
3.2k
views
Tool:
pyGeno 1.2: Python package for Personalized Genomics and Proteomics
python
SNP
rna-seq
dbSNP
ensembl
updated 23 months ago by
Ram
43k • written 9.1 years ago by
Tariq Daouda
▴ 220
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
737 results • Page
2 of 15
Recent Votes
Sequence alignment on split read event such as inversion, duplication and complex nested events.
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
Comment: Add stats to the plot
Post-doctoral Position in Alzheimer’s Disease Genetics, ‘Omics, and Biomarkers
The Biostar Handbook. A bioinformatics e-book for beginners.
Answer: How to add Ensembl id to cluster.markers in Seurat
How to add Ensembl id to cluster.markers in Seurat
Recent Locations •
All
Hong Kong,
just now
United States,
1 minute ago
United States,
4 minutes ago
South Korea,
6 minutes ago
Whitefish, MT,
7 minutes ago
Hong Kong,
11 minutes ago
France,
17 minutes ago
Recent Awards •
All
Scholar
to
Pierre Lindenbaum
161k
Voter
to
Sara
▴ 30
Popular Question
to
carlopecoraro2
★ 2.5k
Popular Question
to
scideas
▴ 30
Popular Question
to
Muhammad
• 0
Popular Question
to
synat.keam
▴ 100
Scholar
to
jv
★ 1.8k
Recent Replies
Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Luqman
• 0
I am using *pybiomart* which has Server inplace of BiomartServer, I used that as per above but still getting the same error. Also, when I a…
Comment: Blastn, need help to increase speed
by
m13113153781
• 0
mmseq2 is indeed a good acceleration solution, but its index files require ~ 6 T space....
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
KHURRAM SHAHZAD
• 0
Thank you it works
Answer: Add stats to the plot
by
Ghada
• 0
I think this is what caused the error. we do not have group 1 and 2 in the statistical test results???? ![enter image description here][…
Answer: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
Bibi
• 0
@atpoint thanks you for your timely response. Can someone else shed light if we can compare the trend of DEGs using the scRNA and Bulk RNA…
Comment: Add stats to the plot
by
GenoMax
142k
Please use `101010` to format `code` so it is represented in monospace font. I have done this for you now.
Answer: is there a tool to recover corrupted fastq files
by
Tommaso
• 0
You may also want to give a try to **FastqWiper** (https://github.com/mazzalab/fastqwiper)
Comment: Add stats to the plot
by
Ghada
• 0
Thanks. That helpful. I am getting this error data4_test <- data4.ts%>% ungroup() %>% t.test(data =.,value ~ Condition)%>% + …
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
ATpoint
82k
I cannot comment here. You are asking why results between two experiments are different. I do not know without seeing the data.
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
Bibi
• 0
Thank you so much for this insight. I just want to clarify another point here. I have used scRNA seq data from mice mammary epithelial cell…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
> Cannot read non-existent file: file:///local/home/User/VCF_Filtering/biostar.code your file doesn't exist, is at the wrong place etc.
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
ajbarrett98
• 0
Hi Pierre, I am attempting to run this code and am running into this error: (jvar) $ jvarkit vcffilterjdk -f biostar.code Dart_VCF2_Or…
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
ATpoint
82k
I cannot give a precise answer, as ML is not my field, but generally, why don't you apply the method to pseudobulks of the exact single-cel…
Answer: geom_bar issue in ggplot2 with xlim()
by
ATpoint
82k
https://stackoverflow.com/questions/10365167/geom-bar-bars-not-displaying-when-specifying-ylim
Comment: What marks a De-Novo Genome assembly as FAILED?
by
Umer
▴ 50
Yes. We are sequencing 45 different samples with illumina. 12 of these are also going to be sequenced with Nanopore (for hybrid assembly). …
Traffic: 1718 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