recipe bioconductor-compcoder

RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods

Homepage

https://bioconductor.org/packages/3.12/bioc/html/compcodeR.html

License

GPL (>= 2)

Recipe

/bioconductor-compcoder/meta.yaml

This package provides extensive functionality for comparing results obtained by different methods for differential expression analysis of RNAseq data. It also contains functions for simulating count data. Finally, it provides convenient interfaces to several packages for performing the differential expression analysis. These can also be used as templates for setting up and running a user-defined differential analysis workflow within the framework of the package.

package bioconductor-compcoder

Versions

1.26.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.20.0-0,  1.18.1-0,  1.18.0-0

Depends

• bioconductor-edger >=3.32.0,<3.33.0

• bioconductor-limma >=3.46.0,<3.47.0

• r-base >=4.0,<4.1.0a0

• r-catools

• r-gdata

• r-ggplot2

• r-gplots

• r-gtools

• r-kernsmooth

• r-knitr >=1.2

• r-lattice >=0.16

• r-markdown

• r-mass

• r-modeest

• r-rocr

• r-sm

• r-stringr

• r-vioplot

Required By

Installation

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

conda install bioconductor-compcoder

and update with:

conda update bioconductor-compcoder

or use the docker container:

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

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