Package: CeTF
Type: Package
Title: Coexpression for Transcription Factors using Regulatory Impact
        Factors and Partial Correlation and Information Theory analysis
Version: 1.6.0
Authors@R: c(person("Carlos Alberto", "Oliveira de Biagi Junior", email = 
  "cbiagijr@gmail.com", role = c("aut", "cre")), person("Ricardo", "Perecin 
  Nociti", email = "rnociti@gmail.com", role = c("aut")), person("Breno", 
  "Osvaldo Funicheli", email = "osvaldobreno99@gmail.com ", role = c("aut")), 
  person("João Paulo", "Bianchi Ximenez", email = "joaopaulo.ximenez@me.com", 
  role = c("ctb")), person("Patrícia", "de Cássia Ruy", email = 
  "patiruy@gmail.com", role = c("ctb")), person("Marcelo", "Gomes de Paula", 
  email = "marcelogomesrp@gmail.com", role = c("ctb")), person("Rafael", "dos 
  Santos Bezerra", email = "rafaelbezerra50@yahoo.com", role = c("ctb")), 
  person("Wilson", "Araújo da Silva Junior", email = "wilsonjr@usp.br", role = 
  c("aut", "ths")))
Description: This package provides the necessary functions for performing the 
  Partial Correlation coefficient with Information Theory (PCIT) (Reverter and 
  Chan 2008) and Regulatory Impact Factors (RIF) (Reverter et al. 2010) 
  algorithm. The PCIT algorithm identifies meaningful correlations to define 
  edges in a weighted network and can be applied to any correlation-based 
  network including but not limited to gene co-expression networks, while the 
  RIF algorithm identify critical Transcription Factors (TF) from gene 
  expression data. These two algorithms when combined provide a very relevant 
  layer of information for gene expression studies (Microarray, RNA-seq and 
  single-cell RNA-seq data).
Imports: circlize, ComplexHeatmap, clusterProfiler, DESeq2, dplyr,
        GenomicTools, GenomicTools.fileHandler, GGally, ggnetwork,
        ggplot2, ggpubr, ggrepel, graphics, grid, igraph, Matrix,
        network, Rcpp, RCy3, stats, SummarizedExperiment, S4Vectors,
        utils
Suggests: airway, kableExtra, knitr, org.Hs.eg.db, rmarkdown, testthat
SystemRequirements: libcurl4-openssl-dev, libxml2-dev, libssl-dev,
        gfortran, build-essential, libz-dev, zlib1g-dev
Depends: R (>= 4.0), methods
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
biocViews: Sequencing, RNASeq, Microarray, GeneExpression,
        Transcription, Normalization, DifferentialExpression,
        SingleCell, Network, Regression, ChIPSeq, ImmunoOncology,
        Coverage
VignetteBuilder: knitr
LinkingTo: Rcpp, RcppArmadillo
git_url: https://git.bioconductor.org/packages/CeTF
git_branch: RELEASE_3_14
git_last_commit: 65513aa
git_last_commit_date: 2021-10-26
Date/Publication: 2021-10-26
NeedsCompilation: yes
Packaged: 2021-10-27 00:36:34 UTC; biocbuild
Author: Carlos Alberto Oliveira de Biagi Junior [aut, cre],
  Ricardo Perecin Nociti [aut],
  Breno Osvaldo Funicheli [aut],
  João Paulo Bianchi Ximenez [ctb],
  Patrícia de Cássia Ruy [ctb],
  Marcelo Gomes de Paula [ctb],
  Rafael dos Santos Bezerra [ctb],
  Wilson Araújo da Silva Junior [aut, ths]
Maintainer: Carlos Alberto Oliveira de Biagi Junior <cbiagijr@gmail.com>
Built: R 4.1.1; i386-w64-mingw32; 2021-10-27 10:11:23 UTC; windows
Archs: i386, x64
