DOI: 10.18129/B9.bioc.CEMiTool  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see CEMiTool.

Co-expression Modules identification Tool

Bioconductor version: 3.16

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 B├╝rger [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")):


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HTML R Script CEMiTool: Co-expression Modules Identification Tool
PDF   Reference Manual


biocViews GeneExpression, GraphAndNetwork, ImmunoOncology, Network, NetworkEnrichment, Pathways, RNASeq, Software, Transcriptomics, mRNAMicroarray
Version 1.22.0
In Bioconductor since BioC 3.6 (R-3.4) (5.5 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
Suggests testthat, BiocManager
Depends On Me
Imports Me
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Source Package CEMiTool_1.22.0.tar.gz
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Bioc Package Browser https://code.bioconductor.org/browse/CEMiTool/
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