recipe bioconductor-cemitool

The CEMiTool package unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.

Homepage

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

License

GPL-3

Recipe

/bioconductor-cemitool/meta.yaml

package bioconductor-cemitool

Versions

1.8.3-0, 1.6.10-0

Depends

• bioconductor-clusterprofiler >=3.12.0,<3.13.0

• bioconductor-fgsea >=1.10.0,<1.11.0

• bioconductor-geneoverlap >=1.20.0,<1.21.0

• bioconductor-limma >=3.40.0,<3.41.0

• r-base >=3.6,<3.7.0a0

• r-data.table >=1.9.4

• r-dplyr

• r-dt

• r-ff

• r-ffbase

• r-ggdendro

• r-ggplot2

• r-ggpmisc

• r-ggrepel

• r-ggthemes

• r-grbase

• r-gridextra

• r-gtable

• r-htmltools

• r-igraph

• r-intergraph

• r-knitr

• r-matrixstats

• r-network

• r-plyr

• r-pracma

• r-rcolorbrewer

• r-rmarkdown

• r-scales

• r-sna

• r-stringr

• r-tidyr

• r-wgcna

Required By

Installation

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

conda install bioconductor-cemitool

and update with:

conda update bioconductor-cemitool

or use the docker container:

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

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