recipe bioconductor-consensusde

This package allows users to perform DE analysis using multiple algorithms. It seeks consensus from multiple methods. Currently it supports “Voom”, “EdgeR” and “DESeq”. It uses RUV-seq (optional) to remove batch effects.

Homepage

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

License

GPL-3

Recipe

/bioconductor-consensusde/meta.yaml

package bioconductor-consensusde

(downloads) docker_bioconductor-consensusde

Versions

1.0.0-0

Depends bioconductor-airway

>=1.2.0,<1.3.0

Depends bioconductor-annotationdbi

>=1.44.0,<1.45.0

Depends bioconductor-biobase

>=2.42.0,<2.43.0

Depends bioconductor-biocparallel

>=1.16.0,<1.17.0

Depends bioconductor-biostrings

>=2.50.0,<2.51.0

Depends bioconductor-deseq2

>=1.22.0,<1.23.0

Depends bioconductor-edaseq

>=2.16.0,<2.17.0

Depends bioconductor-edger

>=3.24.0,<3.25.0

Depends bioconductor-genomicalignments

>=1.18.0,<1.19.0

Depends bioconductor-genomicfeatures

>=1.34.0,<1.35.0

Depends bioconductor-limma

>=3.38.0,<3.39.0

Depends bioconductor-pcamethods

>=1.74.0,<1.75.0

Depends bioconductor-rsamtools

>=1.34.0,<1.35.0

Depends bioconductor-ruvseq

>=1.16.0,<1.17.0

Depends bioconductor-s4vectors

>=0.20.0,<0.21.0

Depends bioconductor-summarizedexperiment

>=1.12.0,<1.13.0

Depends bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene

>=3.2.0,<3.3.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-dendextend

Depends r-rcolorbrewer

Requirements

Installation

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

conda install bioconductor-consensusde

and update with:

conda update bioconductor-consensusde

or use the docker container:

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

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