recipe bioconductor-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.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/DESeq2.html

License

LGPL (>= 3)

Recipe

/bioconductor-deseq2/meta.yaml

Links

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

package bioconductor-deseq2

Versions

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 >=2.44.0,<2.45.0

• bioconductor-biocgenerics >=0.30.0,<0.31.0

• bioconductor-biocparallel >=1.18.0,<1.19.0

• bioconductor-genefilter >=1.66.0,<1.67.0

• bioconductor-geneplotter >=1.62.0,<1.63.0

• bioconductor-genomicranges >=1.36.0,<1.37.0

• bioconductor-iranges >=2.18.0,<2.19.0

• bioconductor-s4vectors >=0.22.0,<0.23.0

• bioconductor-summarizedexperiment >=1.14.0,<1.15.0

• libgcc-ng >=7.3.0

• libstdcxx-ng >=7.3.0

• r-base >=3.6,<3.7.0a0

• r-ggplot2

• r-hmisc

• r-locfit

• r-rcpp >=0.11.0

• r-rcpparmadillo

Required By

• r-empiricalfdr.deseq2

• bioconductor-pcaexplorer

• riborex

• bioconductor-inspect

• bioconductor-snphood

• bioconductor-damirseq

• bioconductor-debrowser

• bioconductor-degreport

• bioconductor-animalcules

• trnanalysis

• bioconductor-singlecelltk

• bioconductor-regionreport

• bioconductor-tcc

• bioconductor-anamir

• bioconductor-diffbind

• bioconductor-anota2seq

• bioconductor-gdcrnatools

• r-sartools

• xtail

• peakachu

• bioconductor-rmmquant

• bioconductor-systempiper

• r-lncpipereporter

• bioconductor-pathostat

• bioconductor-isomirs

• bioconductor-ideal

• bioconductor-srnadiff

• bcbio-rnaseq

• bioconductor-dchiprep

• r-bcbiornaseq

• bioconductor-dexseq

• bioconductor-junctionseq

• bioconductor-impulsede2

• bioconductor-reportingtools

• bioconductor-kissde

• bioconductor-xbseq

• r-ampvis

• r-htssip

• bioconductor-coseq

• bioconductor-decomplexdisease

• bioconductor-anaquin

• bioconductor-countsimqc

• bioconductor-fourcseq

• bioconductor-outrider

• bioconductor-vidger

• bioconductor-deformats

• bioconductor-desubs

• bioconductor-erssa

• bioconductor-genogam

• bioconductor-rnaseqr

• r-riborex

• bioconductor-mlseq

• bioconductor-timeseriesexperiment

• bioconductor-icetea

• bioconductor-rgsepd

• piret

• rapid

• bioconductor-nbamseq

• bioconductor-enrichmentbrowser

• bioconductor-ihwpaper

• r-metalonda

• bioconductor-eegc

• bioconductor-bloodcancermultiomics2017

• bioconductor-powerexplorer

• r-r4cker

• bioconductor-consensusde

• bioconductor-htsfilter

• bioconductor-interest

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)