Package: CEMiTool
Title: Co-expression Modules identification Tool
Version: 1.30.0
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: 7.1.2
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/CEMiTool
git_branch: RELEASE_3_20
git_last_commit: b1ca198
git_last_commit_date: 2024-10-29
Repository: Bioconductor 3.20
Date/Publication: 2024-10-29
NeedsCompilation: no
Packaged: 2024-10-29 23:55:46 UTC; biocbuild
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>
Built: R 4.4.2; ; 2025-01-04 03:49:51 UTC; unix
