Package: CeTF
Type: Package
Title: Coexpression for Transcription Factors using Regulatory Impact
        Factors and Partial Correlation and Information Theory analysis
Version: 1.22.0
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.fileHandler, GGally, ggnetwork, ggplot2, ggpubr,
        ggrepel, graphics, grid, igraph, Matrix, network, Rcpp, RCy3,
        stats, SummarizedExperiment, S4Vectors, utils, methods
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)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.3
biocViews: Sequencing, RNASeq, Microarray, GeneExpression,
        Transcription, Normalization, DifferentialExpression,
        SingleCell, Network, Regression, ChIPSeq, ImmunoOncology,
        Coverage
VignetteBuilder: knitr
LinkingTo: Rcpp, RcppArmadillo
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libicu-dev libpng-dev
        libxml2-dev libssl-dev perl python3 libzmq3-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:56:07 UTC
RemoteUrl: https://github.com/bioc/CeTF
RemoteRef: RELEASE_3_22
RemoteSha: 240816559f33c057c1865e12eaff1cc2b6e1d131
NeedsCompilation: yes
Packaged: 2026-03-09 04:05:42 UTC; root
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 4.5.2; x86_64-w64-mingw32; 2026-03-09 04:09:16 UTC; windows
Archs: x64
