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

(downloads) docker_bioconductor-cemitool

Versions

1.6.10-0

Depends bioconductor-clusterprofiler

>=3.10.0,<3.11.0

Depends bioconductor-fgsea

>=1.8.0,<1.9.0

Depends bioconductor-geneoverlap

>=1.18.0,<1.19.0

Depends bioconductor-limma

>=3.38.0,<3.39.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-data.table

>=1.9.4

Depends r-dplyr

Depends r-dt

Depends r-ff

Depends r-ffbase

Depends r-ggdendro

Depends r-ggplot2

Depends r-ggpmisc

Depends r-ggrepel

Depends r-ggthemes

Depends r-grbase

Depends r-gridextra

Depends r-gtable

Depends r-htmltools

Depends r-igraph

Depends r-intergraph

Depends r-knitr

Depends r-matrixstats

Depends r-network

Depends r-plyr

Depends r-pracma

Depends r-rcolorbrewer

Depends r-rmarkdown

Depends r-scales

Depends r-sna

Depends r-stringr

Depends r-tidyr

Depends r-wgcna

Requirements

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>)