recipe bioconductor-cemitool

Co-expression Modules identification Tool






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 r-base:


depends r-data.table:


depends r-dplyr:

depends r-dt:

depends r-fastcluster:

depends r-ggdendro:

depends r-ggplot2:

depends r-ggpmisc:

depends r-ggrepel:

depends r-ggthemes:

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-pracma:

depends r-rmarkdown:

depends r-scales:

depends r-sna:

depends r-stringr:

depends r-wgcna:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-cemitool

and update with::

   mamba update bioconductor-cemitool

To create a new environment, run:

mamba create --name myenvname bioconductor-cemitool

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

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

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