CEMiTool

This is the development version of CEMiTool; for the stable release version, see CEMiTool.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6

Co-expression Modules identification Tool

Bioconductor version: Development (3.24)

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")):

Pedro Russo, Gustavo Ferreira, Matheus Bürger, Lucas Cardozo, Diogenes Lima, Thiago Hirata, Melissa Lever, Helder Nakaya. CEMiTool: Co-expression Modules identification Tool. doi:10.18129/B9.bioc.CEMiTool, R package version 1.37.0, https://bioconductor.org/packages/CEMiTool.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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	1.37.0
In Bioconductor since	BioC 3.6 (R-3.4) (9 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
System Requirements
URL

Suggests	testthat, BiocManager
Linking To
Enhances
Depends On Me
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Build Report	Build Report, r-universe

Package Archives

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

Source Package	CEMiTool_1.37.0.tar.gz
Windows Binary (x86_64)	CEMiTool_1.37.0.zip
macOS Binary (big-sur-x86_64)	CEMiTool_1.37.0.tgz
macOS Binary (sonoma-arm64)	CEMiTool_1.37.0.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	https://bioconductor.org/packages/CEMiTool/
Package Downloads Report	Download Stats