CEMiTool

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see CEMiTool.

Co-expression Modules identification Tool

Bioconductor version: 3.9

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>

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

Installation

To install this package, start R (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("CEMiTool")

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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, GraphAndNetwork, ImmunoOncology, Network, NetworkEnrichment, Pathways, RNASeq, Software, Transcriptomics, mRNAMicroarray
Version	1.8.3
In Bioconductor since	BioC 3.6 (R-3.4) (6.5 years)
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
System Requirements
URL

Suggests	testthat, BiocManager
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	CEMiTool_1.8.3.tar.gz
Windows Binary	CEMiTool_1.8.3.zip
Mac OS X 10.11 (El Capitan)	CEMiTool_1.8.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CEMiTool
Source Repository (Developer Access)	git clone [email protected]:packages/CEMiTool
Bioc Package Browser	https://code.bioconductor.org/browse/CEMiTool/
Package Short Url	https://bioconductor.org/packages/CEMiTool/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.9	Source Archive