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”, but can be easily extended. It uses RUV-seq (optional) to remove batch effects.

Homepage

https://bioconductor.org/packages/3.8/bioc/html/consensusDE.html

License

GPL-3

Recipe

/bioconductor-consensusde/meta.yaml

package bioconductor-consensusde

Versions

1.0.0-0

Depends

• bioconductor-airway >=1.2.0,<1.3.0

• bioconductor-annotationdbi >=1.44.0,<1.45.0

• bioconductor-biobase >=2.42.0,<2.43.0

• bioconductor-biocparallel >=1.16.0,<1.17.0

• bioconductor-biostrings >=2.50.0,<2.51.0

• bioconductor-deseq2 >=1.22.0,<1.23.0

• bioconductor-edaseq >=2.16.0,<2.17.0

• bioconductor-edger >=3.24.0,<3.25.0

• bioconductor-genomicalignments >=1.18.0,<1.19.0

• bioconductor-genomicfeatures >=1.34.0,<1.35.0

• bioconductor-limma >=3.38.0,<3.39.0

• bioconductor-pcamethods >=1.74.0,<1.75.0

• bioconductor-rsamtools >=1.34.0,<1.35.0

• bioconductor-ruvseq >=1.16.0,<1.17.0

• bioconductor-s4vectors >=0.20.0,<0.21.0

• bioconductor-summarizedexperiment >=1.12.0,<1.13.0

• bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene >=3.2.0,<3.3.0

• r-base >=3.5.1,<3.5.2.0a0

• r-dendextend

• r-rcolorbrewer

Required By

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>)

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-consensusde/README.html)