CeTF

DOI: 10.18129/B9.bioc.CeTF    

This package is for version 3.15 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: 3.15

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>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("CeTF")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("CeTF")

 

HTML	R Script	Analyzing Regulatory Impact Factors and Partial Correlation and Information Theory
PDF		Reference Manual
Text		NEWS

Details

biocViews	ChIPSeq, Coverage, DifferentialExpression, GeneExpression, ImmunoOncology, Microarray, Network, Normalization, RNASeq, Regression, Sequencing, SingleCell, Software, Transcription
Version	1.8.0
In Bioconductor since	BioC 3.11 (R-4.0) (2.5 years)
License	GPL-3
Depends	R (>= 4.0), methods
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
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
Enhances
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	CeTF_1.8.0.tar.gz
Windows Binary	CeTF_1.8.0.zip (64-bit only)
macOS Binary (x86_64)	CeTF_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CeTF
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CeTF
Package Short Url	https://bioconductor.org/packages/CeTF/
Package Downloads Report	Download Stats