CEMiTool

Co-expression Modules identification Tool

Bioconductor version: Release (3.17)

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 "4.3") 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

Details

biocViews	GeneExpression, GraphAndNetwork, ImmunoOncology, Network, NetworkEnrichment, Pathways, RNASeq, Software, Transcriptomics, mRNAMicroarray
Version	1.24.0
In Bioconductor since	BioC 3.6 (R-3.4) (6 years)
License	GPL-3
Depends	R (>= 4.0)
Imports	methods, scales, 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, fastcluster
Linking To
Suggests	testthat, BiocManager
System Requirements
Enhances
URL

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_1.24.0.tar.gz
Windows Binary	CEMiTool_1.24.0.zip
macOS Binary (x86_64)	CEMiTool_1.24.0.tgz
macOS Binary (arm64)	CEMiTool_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CEMiTool
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CEMiTool
Bioc Package Browser	https://code.bioconductor.org/browse/CEMiTool/
Package Short Url	https://bioconductor.org/packages/CEMiTool/
Package Downloads Report	Download Stats