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737 results • Page
2 of 15
Sort: replies
Rank
Views
Votes
Replies
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
4.6k
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
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
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
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
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
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
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
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
7
votes
9
replies
4.1k
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
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
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 8.4 years ago by
Kamil
★ 2.3k
8
votes
8
replies
3.3k
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
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
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
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
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
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
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 11.8 years ago by
Istvan Albert
100k
3
votes
8
replies
741
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
4.4k
views
Tool:
MetaR: a simple language useful for RNA-Seq data analysis
RNA-Seq
R
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
fac2003
▴ 170
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
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
737 results • Page
2 of 15
Recent Votes
ClusterProfiler : What is GeneRatio and BgRatio?
A: ClusterProfiler : What is GeneRatio and BgRatio?
A: ClusterProfiler : What is GeneRatio and BgRatio?
C: Cleaning RNA-Seq data from rRNA
Answer: How to find identical sequences in genome fasta file (by Python or any possible
Merging/Concatenating Vcf Files
Answer: Ti Tv ratio and their usefulness in exome sequencing
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Recent Awards •
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Commentator
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GenoMax
142k
Popular Question
to
safeassli
▴ 10
Popular Question
to
curious
▴ 750
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manaswwm
▴ 510
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Raghad
• 0
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Pierre Lindenbaum
161k
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Sara
▴ 30
Recent Replies
Comment: HGVS Nomenclature of Multiple Indels found in Cis
by
Ram
43k
They're not addressing the actual question, just saying something tangentially related. It looks like their understanding of both consensus…
Comment: Super ehancers
by
Oburah
• 0
python2.7 ROSE_main.py -g HG38 -i /home/hesborn/Desktop/Data/S3vS2-2.gff -r /home/hesborn/Downloads/possorted_bam.bam.bai -o Hezz -s 12500 …
Answer: How to generate an Upset plot in R to plot the shared variants between cell free
by
zx8754
11k
Try this example: library(UpSetR) #example input, 4 samples, 250 variants set.seed(1); d <- data.frame(matrix(sample…
Answer: Illumina methylation EPIC V2 array
by
fu_entomology
▴ 40
We have been using SeSAMe, it works well for the most part. They have an enrichment tool called KnowYourCG. You can check it out their vign…
Answer: How to find identical sequences in genome fasta file (by Python or any possible
by
GenoMax
142k
> My final purpose are find and remove any identical sequences present in my genome fasta file. You can use `clumpify.sh` from BBMap suite…
Comment: GO analysis: Indicate genes corresponding to the pathway
by
marco.barr
▴ 130
I think you have set a filter to get these pahways upstream from the DEG results. You should extract the IDs or names of the genes that you…
Comment: GATK Structural Variants Pipeline - Steps
by
Bioinformatics_begginner
▴ 20
Thank you for the response, I mean those tools aren't all the steps from fasta to vcf. Would be key understanding the aligner, reference us…
Comment: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
GenoMax
142k
Please accept the answer (green check mark) to provide closure to this thread.
Answer: GATK Structural Variants Pipeline - Steps
by
Pierre Lindenbaum
161k
> A structural variation pipeline for short-read sequencing https://github.com/broadinstitute/gatk-sv
Comment: GATK Structural Variants Pipeline - Steps
by
DGTool
▴ 20
If it is just the tools that they used which you are looking for, the first link in the overview section of that page leads to the followin…
Comment: GO analysis: p-value range
by
Matthias Zepper
4.6k
It is just a warning that you add a new scale to a ggplot2 plot, that already has an existing one, which will get replaced. Nothing to worr…
Comment: GO analysis: p-value range
by
marco.barr
▴ 130
If you write me the code you used I can help you more
Comment: GO analysis: p-value range
by
sooni
▴ 20
When I run the code, the following message appears: Scale for y is already present. Adding another scale for y, which will replace…
Comment: Why most genes have high padj values
by
mnx0723
• 0
In the case of other samples, the total number of genes is at least 3,000 more than that one, but it seems to be a relatively small number.…
Comment: How to hide label in layout file of MCscan (python version)
by
jinyi
• 0
Command line is as follows: python -m jcvi.graphics.synteny Cs.Cm.i1.blocks Cs_Cm.bed layout2.txt
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