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("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 |
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 |
See More
| 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 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 3.9 | Source Archive |