recipe bioconductor-deseq2

Differential gene expression analysis based on the negative binomial distribution

Homepage

https://bioconductor.org/packages/3.14/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

1.34.0-0,  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, 

1.34.0-0,  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 >=2.54.0,<2.55.0

• bioconductor-biocgenerics >=0.40.0,<0.41.0

• bioconductor-biocparallel >=1.28.0,<1.29.0

• bioconductor-genefilter >=1.76.0,<1.77.0

• bioconductor-geneplotter >=1.72.0,<1.73.0

• bioconductor-genomicranges >=1.46.0,<1.47.0

• bioconductor-iranges >=2.28.0,<2.29.0

• bioconductor-s4vectors >=0.32.0,<0.33.0

• bioconductor-summarizedexperiment >=1.24.0,<1.25.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=9.4.0

• liblapack >=3.8.0,<4.0a0

• libstdcxx-ng >=9.4.0

• r-base >=4.1,<4.2.0a0

• r-ggplot2

• r-locfit

• r-rcpp >=0.11.0

• r-rcpparmadillo

Required By

• r-deseqanalysis

• r-tmae

• bioconductor-dewseq

• bioconductor-crossmeta

• bioconductor-kissde

• bioconductor-systempipetools

• r-metalonda

• bioconductor-htsfilter

• bioconductor-multisight

• tetranscripts

• bioconductor-pcaexplorer

• bioconductor-cetf

• bioconductor-snphood

• bioconductor-phantasus

• r-htssip

• bioconductor-microbiomeexplorer

• bioconductor-rgsepd

• bioconductor-vulcan

• bioconductor-scgps

• bioconductor-spatialheatmap

• bioconductor-scbfa

• peakachu

• bioconductor-bionero

• bioconductor-ebsea

• r-ampvis

• drop

• bioconductor-orfik

• bioconductor-regionreport

• mosca

• hamip

• bioconductor-singlecelltk

• bioconductor-animalcules

• bioconductor-exomepeak2

• flair

• bioconductor-countsimqc

• bioconductor-ribodipa

• bioconductor-circrnaprofiler

• bioconductor-muscat

• bioconductor-genetonic

• bioconductor-icetea

• bioconductor-anota2seq

• rapid

• bioconductor-gdcrnatools

• trnanalysis

• bioconductor-tbsignatureprofiler

• bioconductor-proactiv

• bioconductor-timeseriesexperiment

• bioconductor-brgenomics

• bioconductor-desubs

• bioconductor-anaquin

• bioconductor-benchdamic

• mimseq

• bioconductor-easier

• r-riborex

• bioconductor-microbiomemarker

• bioconductor-degreport

• bioconductor-rnaseqr

• bioconductor-erssa

• bioconductor-deltacapturec

• cmsip

• bioconductor-genogam

• bioconductor-umi4cats

• bioconductor-consensusde

• bioconductor-mlseq

• r-r4cker

• bioconductor-translatome

• bioconductor-damirseq

• bioconductor-reportingtools

• bioconductor-regenrich

• bioconductor-seqgsea

• bioconductor-decomplexdisease

• bioconductor-dexseq

• bioconductor-vidger

• bcbio-rnaseq

• bioconductor-ideal

• bioconductor-interest

• r-lncpipereporter

• bioconductor-outrider

• bioconductor-diffbind

• bioconductor-apalyzer

• bioconductor-glimma

• ssdrippipeline

• bioconductor-debrowser

• bioconductor-srnadiff

• bioconductor-tcc

• bioconductor-eegc

• bioconductor-inspect

• r-sartools

• bioconductor-nbamseq

• bioconductor-fieldeffectcrc

• bioconductor-ihwpaper

• r-bcbiornaseq

• bioconductor-coseq

• bioconductor-isomirs

• bioconductor-pathostat

• piret

• bioconductor-rmmquant

• bioconductor-deformats

• bioconductor-metaseqr2

• bioconductor-setools

• bioconductor-bloodcancermultiomics2017

• r-empiricalfdr.deseq2

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>)

Download stats

Link to this page

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