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 (3.8)

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 and enter:

if (!requireNamespace("BiocManager", quietly=TRUE))
BiocManager::install("CEMiTool", version = "devel")


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, Network, NetworkEnrichment, Pathways, RNASeq, Software, Transcriptomics, mRNAMicroarray
Version 1.5.0
License GPL-3
Depends R (>= 3.4)
Imports methods, scales, gRbase, 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
Suggests testthat
Depends On Me
Imports Me
Suggests Me
Build Report  

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

Source Package CEMiTool_1.5.0.tar.gz
Windows Binary CEMiTool_1.5.0.zip
Mac OS X 10.11 (El Capitan) CEMiTool_1.5.0.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 http://bioconductor.org/packages/CEMiTool/
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