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CeTF

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


Bioconductor version: Release (3.18)

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>

Citation (from within R, enter citation("CeTF")):

Installation

To install this package, start R (version "4.3") 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")
Analyzing Regulatory Impact Factors and Partial Correlation and Information Theory HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ChIPSeq, Coverage, DifferentialExpression, GeneExpression, ImmunoOncology, Microarray, Network, Normalization, RNASeq, Regression, Sequencing, SingleCell, Software, Transcription
Version 1.14.0
In Bioconductor since BioC 3.11 (R-4.0) (4 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
System Requirements libcurl4-openssl-dev, libxml2-dev, libssl-dev, gfortran, build-essential, libz-dev, zlib1g-dev
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Suggests airway, kableExtra, knitr, org.Hs.eg.db, rmarkdown, testthat
Linking To Rcpp, RcppArmadillo
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Package Archives

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

Source Package CeTF_1.14.0.tar.gz
Windows Binary CeTF_1.14.0.zip
macOS Binary (x86_64) CeTF_1.14.0.tgz
macOS Binary (arm64) CeTF_1.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CeTF
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CeTF
Bioc Package Browser https://code.bioconductor.org/browse/CeTF/
Package Short Url https://bioconductor.org/packages/CeTF/
Package Downloads Report Download Stats