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.






package bioconductor-cemitool

(downloads) docker_bioconductor-cemitool



Depends bioconductor-clusterprofiler


Depends bioconductor-fgsea


Depends bioconductor-geneoverlap


Depends bioconductor-limma


Depends r-base


Depends r-data.table


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



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<tag>

(see bioconductor-cemitool/tags for valid values for <tag>)