recipe bioconductor-edger

Empirical Analysis of Digital Gene Expression Data in R

Homepage

https://bioconductor.org/packages/3.11/bioc/html/edgeR.html

License

GPL (>=2)

Recipe

/bioconductor-edger/meta.yaml

Links

biotools: edger

Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce read counts, including ChIP-seq, ATAC-seq, Bisulfite-seq, SAGE and CAGE.

package bioconductor-edger

Versions

3.30.0-0, 3.28.0-1, 3.28.0-0, 3.26.5-0, 3.26.0-0, 3.24.3-0, 3.24.1-0, 3.22.5-0, 3.20.7-0, 3.20.1-0, 3.20.0-0, 3.18.1-0, 3.16.5-0, 3.14.0-1, 3.14.0-0, 3.12.1-1, 3.12.1-0, 3.12.0-0, 3.10.5-0

Depends

• bioconductor-limma >=3.44.0,<3.45.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=7.3.0

• liblapack >=3.8.0,<3.9.0a0

• libstdcxx-ng >=7.3.0

• r-base >=4.0,<4.1.0a0

• r-locfit

• r-rcpp

Required By

• bioconductor-tcc

• r-riborex

• bioconductor-splatter

• bioconductor-singscore

• bioconductor-migsa

• bioconductor-consensusde

• r-htscluster

• r-metalonda

• bioconductor-cnvranger

• bioconductor-rcm

• bioconductor-medips

• bioconductor-pathostat

• bioconductor-gdcrnatools

• bioconductor-maaslin2

• bioconductor-eisar

• bioconductor-mlseq

• bioconductor-erssa

• bioconductor-msgbsr

• cap-mirseq

• bioconductor-drimseq

• bioconductor-affycoretools

• bioconductor-msmstests

• bioconductor-systempiper

• bioconductor-erccdashboard

• bioconductor-glimma

• bioconductor-rnaseqr

• bioconductor-csaw

• bioconductor-bioqc

• bioconductor-atacseqqc

• bioconductor-reactomegsa.data

• biotradis

• bioconductor-zinbwave

• bioconductor-proper

• bioconductor-easyrnaseq

• bioconductor-decomplexdisease

• bioconductor-knowseq

• bioconductor-multihiccompare

• bioconductor-timeseriesexperiment

• bioconductor-deformats

• bioconductor-ebsea

• bioconductor-scran

• bioconductor-nbsplice

• bioconductor-desubs

• peakachu

• bioconductor-tweedeseq

• bioconductor-coseq

• bioconductor-diffbind

• bioconductor-rnaseqmap

• bioconductor-interest

• bioconductor-compcoder

• bioconductor-clusterexperiment

• bioconductor-methylmnm

• bioconductor-scde

• bioconductor-muscat

• bioconductor-rnaseqsamplesizedata

• bioconductor-metaseqr2

• bioconductor-arrayexpresshts

• bioconductor-diffcyt

• bioconductor-edda

• bioconductor-icetea

• r-sartools

• bioconductor-gseabenchmarker

• bioconductor-stategra

• bioconductor-simd

• bioconductor-egsea

• bioconductor-tcseq

• bioconductor-diffloop

• bioconductor-diffhic

• bioconductor-awfisher

• bioconductor-enrichmentbrowser

• bioconductor-tradeseq

• bioconductor-metaseqr

• r-lncpipereporter

• piret

• bioconductor-degreport

• maaslin2

• bioconductor-aspli

• bioconductor-singlecellsignalr

• bioconductor-htsfilter

• bioconductor-circrnaprofiler

• bioconductor-dropletutils

• bioconductor-regsplice

• bioconductor-reportingtools

• bioconductor-translatome

• bioconductor-samexplorer

• bioconductor-ruvseq

• riborex

• bioconductor-countsimqc

• bioconductor-damirseq

• bioconductor-bayseq

• bioconductor-psichomics

• bioconductor-setools

• bioconductor-dittoseq

• bioconductor-infercnv

• bioconductor-doser

• bioconductor-tbsignatureprofiler

• bioconductor-scone

• bioconductor-yarn

• bioconductor-isoformswitchanalyzer

• multigps

• bioconductor-tcgabiolinks

• bioconductor-dmrcate

• bioconductor-sva

• bioconductor-repitools

• bioconductor-anota2seq

• bioconductor-dbchip

• r-bcbiornaseq

• bioconductor-debrowser

• bcbio-rnaseq

• bioconductor-svaplsseq

• bioconductor-vidger

• bioconductor-eegc

• bioconductor-roseq

• epicseg

Installation

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

conda install bioconductor-edger

and update with:

conda update bioconductor-edger

or use the docker container:

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

(see bioconductor-edger/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-edger/README.html)