recipe bioconductor-edger

Empirical Analysis of Digital Gene Expression Data in R

Homepage

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

License

GPL (>=2)

Recipe

/bioconductor-edger/meta.yaml

Links

biotools: edger, usegalaxy-eu: 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

3.34.0-0,  3.32.1-0,  3.32.0-0,  3.30.0-0,  3.28.0-1,  3.28.0-0,  3.26.5-0,  3.26.0-0,  3.24.3-0, 

3.34.0-0,  3.32.1-0,  3.32.0-0,  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 >=3.48.0,<3.49.0

• 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-locfit

• r-rcpp

Required By

• bioconductor-damirseq

• bioconductor-diffcyt

• bioconductor-clusterexperiment

• bioconductor-emtdata

• bioconductor-consensusde

• bioconductor-anota2seq

• bioconductor-singlecellsignalr

• bioconductor-medips

• r-lncpipereporter

• r-metalonda

• r-riborex

• bioconductor-atacseqqc

• bioconductor-aspli

• bioconductor-csaw

• bioconductor-compcoder

• bioconductor-spsimseq

• bioconductor-multihiccompare

• bioconductor-maaslin2

• cap-mirseq

• bioconductor-scone

• bioconductor-moanin

• bioconductor-srnadiff

• bioconductor-tcseq

• bioconductor-cnvranger

• bioconductor-deformats

• bioconductor-ruvseq

• bioconductor-coseq

• bioconductor-scran

• bioconductor-tweedeseq

• bioconductor-vidger

• bioconductor-affycoretools

• bioconductor-autonomics

• bcbio-rnaseq

• mosca

• bioconductor-dce

• bioconductor-rnaseqsamplesize

• bioconductor-crossmeta

• bioconductor-bayseq

• bioconductor-muscat

• bioconductor-rnaseqr

• multigps

• bioconductor-methylmnm

• bioconductor-eisar

• bioconductor-samexplorer

• bioconductor-tradeseq

• bioconductor-gseabenchmarker

• bioconductor-psichomics

• bioconductor-interest

• bioconductor-singscore

• peakachu

• bioconductor-setools

• bioconductor-tbsignatureprofiler

• bioconductor-bioqc

• trinity

• bioconductor-awfisher

• bioconductor-rnaseqsamplesizedata

• bioconductor-spatialheatmap

• bioconductor-dropletutils

• bioconductor-reportingtools

• bioconductor-sccb2

• bioconductor-ppcseq

• bioconductor-systempiper

• bioconductor-milor

• bioconductor-dmrcate

• bioconductor-diffutr

• bioconductor-regsplice

• bioconductor-simd

• bioconductor-sva

• bioconductor-doser

• bioconductor-chromscape

• bioconductor-eegc

• bioconductor-decomplexdisease

• bioconductor-reactomegsa.data

• bioconductor-degreport

• bioconductor-gdcrnatools

• maaslin2

• bioconductor-debrowser

• bioconductor-msmstests

• bioconductor-rcm

• bioconductor-desubs

• epicseg

• bioconductor-pathostat

• bioconductor-diffhic

• bioconductor-censcyt

• bioconductor-metaseqr2

• bioconductor-drimseq

• bioconductor-proper

• bioconductor-nbsplice

• bioconductor-arrayexpresshts

• bioconductor-splatter

• bioconductor-scde

• r-bcbiornaseq

• bioconductor-knowseq

• bioconductor-isoformswitchanalyzer

• bioconductor-roseq

• bioconductor-htsfilter

• bioconductor-egsea

• bioconductor-timeseriesexperiment

• bioconductor-stategra

• bioconductor-msgbsr

• bioconductor-diffloop

• r-htscluster

• piret

• bioconductor-circrnaprofiler

• bioconductor-translatome

• bioconductor-yarn

• bioconductor-infercnv

• biotradis

• bioconductor-countsimqc

• r-sartools

• bioconductor-glimma

• bioconductor-erccdashboard

• riborex

• bioconductor-zinbwave

• bioconductor-easyrnaseq

• bioconductor-migsa

• bioconductor-mlseq

• bioconductor-tcc

• bioconductor-icetea

• bioconductor-repitools

• bioconductor-erssa

• bioconductor-phipdata

• bioconductor-enrichmentbrowser

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)