CEMiTool
Co-expression Modules identification Tool
Bioconductor version: 3.23 · Package version: 1.36.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CEMiTool")Details
| Maintainer | Helder Nakaya <hnakaya@usp.br> |
| 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] |
| License | GPL-3 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneExpression, GraphAndNetwork, ImmunoOncology, Network, NetworkEnrichment, Pathways, RNASeq, Software, Transcriptomics, mRNAMicroarray |
| Package Short Url | https://bioconductor.org/packages/CEMiTool/ |
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 1.36.0, https://bioconductor.org/packages/CEMiTool.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | CEMiTool_1.36.0.tar.gz |
| Windows binary (x86_64) | CEMiTool_1.36.0.zip |
| macOS binary (arm64) | CEMiTool_1.36.0.tgz |
| macOS binary (x86_64) | CEMiTool_1.36.0.tgz |
Dependencies
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
Suggests: testthat, BiocManager