DOI: 10.18129/B9.bioc.CEMiTool    

This is the development version of CEMiTool; for the stable release version, see CEMiTool.

Co-expression Modules identification Tool

Bioconductor version: Development (3.12)

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.

Author: Pedro Russo [aut], Gustavo Ferreira [aut], Matheus B├╝rger [aut], Lucas Cardozo [aut], Diogenes Lima [aut], Thiago Hirata [aut], Melissa Lever [aut], Helder Nakaya [aut, cre]

Maintainer: Helder Nakaya <hnakaya at usp.br>

Citation (from within R, enter citation("CEMiTool")):


To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script CEMiTool: Co-expression Modules Identification Tool
PDF   Reference Manual


biocViews GeneExpression, GraphAndNetwork, ImmunoOncology, Network, NetworkEnrichment, Pathways, RNASeq, Software, Transcriptomics, mRNAMicroarray
Version 1.13.2
In Bioconductor since BioC 3.6 (R-3.4) (3 years)
License GPL-3
Depends R (>= 4.0)
Imports methods, scales, dplyr, data.table (>= 1.9.4), WGCNA, grid, ggplot2, ggpmisc, ggthemes, ggrepel, sna, clusterProfiler, fgsea, stringr, knitr, rmarkdown, igraph, DT, htmltools, pracma, intergraph, grDevices, utils, network, matrixStats, ggdendro, gridExtra, gtable, fastcluster
Suggests testthat, BiocManager
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CEMiTool_1.13.2.tar.gz
Windows Binary CEMiTool_1.13.2.zip
macOS 10.13 (High Sierra) CEMiTool_1.13.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/CEMiTool
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CEMiTool
Package Short Url https://bioconductor.org/packages/CEMiTool/
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: