Package: CEMiTool
Title: Co-expression Modules identification Tool
Version: 1.8.3
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 (>= 3.5)
Imports: methods, scales, gRbase, 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, GeneOverlap, limma,
        tidyr, plyr, ff, ffbase, RColorBrewer
Suggests: testthat, BiocManager
License: GPL-3
Encoding: UTF-8
biocViews: GeneExpression, Transcriptomics, GraphAndNetwork,
        mRNAMicroarray, RNASeq, Network, NetworkEnrichment, Pathways,
        ImmunoOncology
LazyData: true
RoxygenNote: 6.1.1
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/CEMiTool
git_branch: RELEASE_3_9
git_last_commit: 295c7f1
git_last_commit_date: 2019-07-10
Date/Publication: 2019-07-11
NeedsCompilation: no
Packaged: 2019-07-12 04:30:10 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 3.6.0; ; 2019-07-12 12:23:56 UTC; windows
