To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("CEMiTool")

In most cases, you don't need to download the package archive at all.

CEMiTool

 

This is the development version of CEMiTool; to use it, please install the devel version of Bioconductor.

Co-expression Modules identification Tool

Bioconductor version: Development (3.6)

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], Helder Nakaya [aut, cre], Matheus B├╝rger [aut], Lucas Cardozo [aut]

Maintainer: Helder Nakaya <hnakaya at usp.br>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("CEMiTool")

Documentation

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

Details

biocViews GeneExpression, GraphAndNetwork, Network, NetworkEnrichment, RNASeq, Software, Transcriptomics, mRNAMicroarray
Version 0.99.9
In Bioconductor since BioC 3.6 (R-3.4)
License GPL-3
Depends R (>= 3.4)
Imports methods, scales, gRbase, data.table (>= 1.9.4), WGCNA, ggplot2, ggrepel, sna, GSEABase, clusterProfiler, fgsea, stringr, knitr, rmarkdown, igraph, DT, htmltools, pracma, intergraph, grDevices, utils, network, matrixStats
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Build Report  

Package Archives

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

Package Source CEMiTool_0.99.9.tar.gz
Windows Binary CEMiTool_0.99.9.zip
Mac OS X 10.11 (El Capitan) CEMiTool_0.99.9.tgz
Source Repository git clone https://git.bioconductor.org/packages/CEMiTool
Package Short Url http://bioconductor.org/packages/CEMiTool/
Package Downloads Report Download Stats

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