CEMiTool
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see CEMiTool.
Co-expression Modules identification Tool
Bioconductor version: 3.11
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("CEMiTool")
):
Installation
To install this package, start R (version "4.0") 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 |
Details
biocViews | GeneExpression, GraphAndNetwork, ImmunoOncology, Network, NetworkEnrichment, Pathways, RNASeq, Software, Transcriptomics, mRNAMicroarray |
Version | 1.12.2 |
In Bioconductor since | BioC 3.6 (R-3.4) (6.5 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 |
See More
Suggests | testthat, BiocManager |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
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Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | CEMiTool_1.12.2.tar.gz |
Windows Binary | CEMiTool_1.12.2.zip |
macOS 10.13 (High Sierra) | CEMiTool_1.12.2.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 |
Old Source Packages for BioC 3.11 | Source Archive |