CeTF
This package is for version 3.11 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: 3.11
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("CeTF")):
Installation
To install this package, start R (version "4.0") 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 | ||
| NEWS | Text |
Details
| biocViews | ChIPSeq, Coverage, DifferentialExpression, GeneExpression, ImmunoOncology, Microarray, Network, Normalization, RNASeq, Regression, Sequencing, SingleCell, Software, Transcription |
| Version | 1.0.7 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4 years) |
| License | GPL-3 |
| Depends | R (>= 4.0), methods |
| Imports | circlize, ComplexHeatmap, clusterProfiler, DESeq2, GenomicTools, GenomicTools.fileHandler, ggnetwork, GGally, ggplot2, ggpubr, ggrepel, graphics, grid, igraph, Matrix, network, Rcpp, RCy3, S4Vectors, stats, SummarizedExperiment, utils, WebGestaltR |
| System Requirements | |
| URL |
See More
| Suggests | airway, kableExtra, knitr, org.Hs.eg.db, rmarkdown, testthat |
| Linking To | Rcpp, RcppArmadillo |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CeTF_1.0.7.tar.gz |
| Windows Binary | CeTF_1.0.7.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | CeTF_1.0.7.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 |
| Old Source Packages for BioC 3.11 | Source Archive |