recipe bioconductor-deseq2

Differential gene expression analysis based on the negative binomial distribution

Homepage

https://bioconductor.org/packages/3.13/bioc/html/DESeq2.html

License

LGPL (>= 3)

Recipe

/bioconductor-deseq2/meta.yaml

Links

biotools: deseq2, doi: 10.1186/s13059-014-0550-8, usegalaxy-eu: deseq2

Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.

package bioconductor-deseq2

Versions

1.32.0-0,  1.30.1-0,  1.30.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.22.1-0,  1.20.0-0,  1.18.1-1, 

1.32.0-0,  1.30.1-0,  1.30.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.22.1-0,  1.20.0-0,  1.18.1-1,  1.18.0-0,  1.16.1-3,  1.16.1-2,  1.16.1-0,  1.14.1-0,  1.12.4-5,  1.12.4-4,  1.12.4-3,  1.12.4-2,  1.12.4-1,  1.10.1-0,  1.10.0-1,  1.10.0-0,  1.8.2-0

Depends

• bioconductor-biobase >=2.52.0,<2.53.0

• bioconductor-biocgenerics >=0.38.0,<0.39.0

• bioconductor-biocparallel >=1.26.0,<1.27.0

• bioconductor-genefilter >=1.74.0,<1.75.0

• bioconductor-geneplotter >=1.70.0,<1.71.0

• bioconductor-genomicranges >=1.44.0,<1.45.0

• bioconductor-iranges >=2.26.0,<2.27.0

• bioconductor-s4vectors >=0.30.0,<0.31.0

• bioconductor-summarizedexperiment >=1.22.0,<1.23.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=9.3.0

• liblapack >=3.8.0,<4.0a0

• libstdcxx-ng >=9.3.0

• r-base >=4.1,<4.2.0a0

• r-ggplot2

• r-locfit

• r-rcpp >=0.11.0

• r-rcpparmadillo

Required By

• bioconductor-damirseq

• bioconductor-consensusde

• bioconductor-anota2seq

• bioconductor-diffbind

• bioconductor-bionero

• r-lncpipereporter

• r-htssip

• r-metalonda

• r-riborex

• bioconductor-pcaexplorer

• bioconductor-fieldeffectcrc

• r-tmae

• bioconductor-dewseq

• bioconductor-exomepeak2

• bioconductor-srnadiff

• r-deseqanalysis

• bioconductor-deformats

• bioconductor-coseq

• bioconductor-ideal

• bioconductor-outrider

• bioconductor-vidger

• bioconductor-microbiomeexplorer

• bioconductor-xbseq

• bioconductor-bloodcancermultiomics2017

• bioconductor-isomirs

• bcbio-rnaseq

• mosca

• tetranscripts

• bioconductor-rmmquant

• bioconductor-crossmeta

• bioconductor-rnaseqr

• bioconductor-dexseq

• bioconductor-muscat

• bioconductor-seqgsea

• hamip

• bioconductor-ebsea

• bioconductor-singlecelltk

• flair

• bioconductor-interest

• peakachu

• bioconductor-setools

• mimseq

• bioconductor-tbsignatureprofiler

• r-ampvis

• bioconductor-genetonic

• trnanalysis

• bioconductor-spatialheatmap

• bioconductor-reportingtools

• bioconductor-umi4cats

• bioconductor-systempiper

• bioconductor-scgps

• bioconductor-scbfa

• bioconductor-regionreport

• bioconductor-eegc

• bioconductor-decomplexdisease

• bioconductor-proactiv

• bioconductor-vulcan

• cmsip

• bioconductor-degreport

• bioconductor-gdcrnatools

• bioconductor-debrowser

• bioconductor-desubs

• bioconductor-pathostat

• bioconductor-kissde

• bioconductor-metaseqr2

• xtail

• bioconductor-systempipetools

• bioconductor-animalcules

• bioconductor-regenrich

• r-r4cker

• bioconductor-deltacapturec

• bioconductor-snphood

• r-bcbiornaseq

• bioconductor-nbamseq

• bioconductor-cetf

• bioconductor-inspect

• bioconductor-htsfilter

• bioconductor-rgsepd

• bioconductor-ribodipa

• bioconductor-multisight

• bioconductor-apalyzer

• bioconductor-timeseriesexperiment

• rapid

• piret

• bioconductor-phantasus

• bioconductor-circrnaprofiler

• bioconductor-translatome

• bioconductor-orfik

• bioconductor-anaquin

• bioconductor-countsimqc

• r-empiricalfdr.deseq2

• r-sartools

• bioconductor-glimma

• riborex

• drop

• bioconductor-mlseq

• bioconductor-tcc

• bioconductor-icetea

• bioconductor-brgenomics

• bioconductor-erssa

• bioconductor-fourcseq

• bioconductor-ihwpaper

• bioconductor-genogam

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-deseq2

and update with:

conda update bioconductor-deseq2

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-deseq2:<tag>

(see bioconductor-deseq2/tags for valid values for <tag>)

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-deseq2/README.html)