DESCRIPTION

Package: CEMiTool
Title: Co-expression Modules identification Tool
Version: 1.27.1
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