CEMiTool

DOI: 10.18129/B9.bioc.CEMiTool    

Co-expression Modules identification Tool

Bioconductor version: Release (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")):

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("CEMiTool", version = "3.8")

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

Documentation

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

browseVignettes("CEMiTool")

 

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

Details

biocViews GeneExpression, GraphAndNetwork, ImmunoOncology, Network, NetworkEnrichment, Pathways, RNASeq, Software, Transcriptomics, mRNAMicroarray
Version 1.6.7
License GPL-3
Depends R (>= 3.5)
Imports methods, scales, gRbase, 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, GeneOverlap, limma, tidyr, plyr, ff, ffbase, RColorBrewer
LinkingTo
Suggests testthat, BiocManager
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Depends On Me
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Build Report  

Package Archives

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

Source Package CEMiTool_1.6.7.tar.gz
Windows Binary CEMiTool_1.6.7.zip
Mac OS X 10.11 (El Capitan) CEMiTool_1.6.7.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/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.8 Source Archive

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