CEMiTool

DOI: 10.18129/B9.bioc.CEMiTool    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see CEMiTool.

Co-expression Modules identification Tool

Bioconductor version: 3.7

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 Bürger [aut], Lucas Cardozo [aut], Diogenes Lima [aut], Thiago Hirata [aut], Melissa Lever [aut], Helder Nakaya [aut, cre]

Maintainer: Helder Nakaya <hnakaya at usp.br>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CEMiTool")

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, Network, NetworkEnrichment, Pathways, RNASeq, Software, Transcriptomics, mRNAMicroarray
Version	1.4.2
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
LinkingTo
Suggests	testthat
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Build Report

Package Archives

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

Source Package	CEMiTool_1.4.2.tar.gz
Windows Binary	CEMiTool_1.4.2.zip
Mac OS X 10.11 (El Capitan)	CEMiTool_1.4.2.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	http://bioconductor.org/packages/CEMiTool/
Package Downloads Report	Download Stats