DOI: 10.18129/B9.bioc.CeTF  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see CeTF.

Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis

Bioconductor version: 3.17

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).

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 at gmail.com>

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biocViews ChIPSeq, Coverage, DifferentialExpression, GeneExpression, ImmunoOncology, Microarray, Network, Normalization, RNASeq, Regression, Sequencing, SingleCell, Software, Transcription
Version 1.12.0
In Bioconductor since BioC 3.11 (R-4.0) (3.5 years)
License GPL-3
Depends R (>= 4.0)
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
LinkingTo Rcpp, RcppArmadillo
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
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Source Package CeTF_1.12.0.tar.gz
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