recipe bioconductor-consensusde

RNA-seq analysis using multiple algorithms

Homepage

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

License

GPL-3

Recipe

/bioconductor-consensusde/meta.yaml

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 unwanted sources of variation.

package bioconductor-consensusde

Versions

1.6.0-0,  1.4.0-1,  1.2.1-0,  1.0.0-0

Depends

• bioconductor-airway >=1.8.0,<1.9.0

• bioconductor-annotationdbi >=1.50.0,<1.51.0

• bioconductor-biobase >=2.48.0,<2.49.0

• bioconductor-biocgenerics >=0.34.0,<0.35.0

• bioconductor-biocparallel >=1.22.0,<1.23.0

• bioconductor-biostrings >=2.56.0,<2.57.0

• bioconductor-deseq2 >=1.28.0,<1.29.0

• bioconductor-edaseq >=2.22.0,<2.23.0

• bioconductor-edger >=3.30.0,<3.31.0

• bioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0

• bioconductor-ensembldb >=2.12.0,<2.13.0

• bioconductor-genomicalignments >=1.24.0,<1.25.0

• bioconductor-genomicfeatures >=1.40.0,<1.41.0

• bioconductor-limma >=3.44.0,<3.45.0

• bioconductor-org.hs.eg.db >=3.11.0,<3.12.0

• bioconductor-pcamethods >=1.80.0,<1.81.0

• bioconductor-rsamtools >=2.4.0,<2.5.0

• bioconductor-ruvseq >=1.22.0,<1.23.0

• bioconductor-s4vectors >=0.26.0,<0.27.0

• bioconductor-summarizedexperiment >=1.18.0,<1.19.0

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

• r-base >=4.0,<4.1.0a0

• r-data.table

• 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)