CEMiTool
This is thereleased version of CEMiTool; for the devel version, seeCEMiTool.
Co-expression Modules identification Tool
Bioconductor version: Release (3.22)
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 "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("CEMiTool")For older versions of R, please refer to the appropriateBioconductor 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 | 1.34.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (8 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 | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | CEMiTool_1.34.0.tar.gz |
| Windows Binary (x86_64) | CEMiTool_1.34.0.zip (64-bit only) |
| macOS Binary (x86_64) | CEMiTool_1.34.0.tgz |
| macOS Binary (arm64) | CEMiTool_1.34.0.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 |