Package: CEMiTool
Title: Co-expression Modules identification Tool
Version: 1.37.0
Authors@R: c( person("Pedro", "Russo", email = "pedro.russo@usp.br",
        role = c("aut")), person("Gustavo", "Ferreira", email =
        "gustavo.rodrigues.ferreira@usp.br", role = c("aut")),
        person("Matheus", "Bürger", email ="burger@usp.br", role 
		= c("aut")), person("Lucas", "Cardozo", email = 
		"lucas.cardozo@usp.br", role = c("aut")), person("Diogenes", "Lima", 
		email = "diogenes.lima@usp.br", role = c("aut")), person("Thiago", 
		"Hirata", email = "thiago.hirata@usp.br", role = c("aut")), 
		person("Melissa", "Lever", email = "melissa.lever@usp.br", 
		role = c("aut")), person("Helder", "Nakaya", email = "hnakaya@usp.br", 
		role = c("aut", "cre")))
Description: 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.
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
License: GPL-3
Encoding: UTF-8
biocViews: GeneExpression, Transcriptomics, GraphAndNetwork,
        mRNAMicroarray, RNASeq, Network, NetworkEnrichment, Pathways,
        ImmunoOncology
LazyData: true
RoxygenNote: 7.3.3
VignetteBuilder: knitr
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:46:09 UTC
RemoteUrl: https://github.com/bioc/CEMiTool
RemoteRef: HEAD
RemoteSha: dffeb392d57fc0cc1a1aaca7168fc297e64457a6
NeedsCompilation: no
Packaged: 2026-07-14 06:16:53 UTC; root
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@usp.br>