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RegEnrich

This is the development version of RegEnrich; for the stable release version, see RegEnrich.

Gene regulator enrichment analysis


Bioconductor version: Development (3.19)

This package is a pipeline to identify the key gene regulators in a biological process, for example in cell differentiation and in cell development after stimulation. There are four major steps in this pipeline: (1) differential expression analysis; (2) regulator-target network inference; (3) enrichment analysis; and (4) regulators scoring and ranking.

Author: Weiyang Tao [cre, aut], Aridaman Pandit [aut]

Maintainer: Weiyang Tao <weiyangtao1513 at gmail.com>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("RegEnrich")

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("RegEnrich")
Gene regulator enrichment with RegEnrich HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, FunctionalPrediction, GeneExpression, GeneSetEnrichment, GeneTarget, Network, NetworkEnrichment, NetworkInference, RNASeq, Software, Transcription, Transcriptomics, TwoChannel
Version 1.13.4
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL (>= 2)
Depends R (>= 4.0.0), S4Vectors, dplyr, tibble, BiocSet, SummarizedExperiment
Imports randomForest, fgsea, DOSE, BiocParallel, DESeq2, limma, WGCNA, ggplot2 (>= 2.2.0), methods, reshape2, magrittr, BiocStyle
System Requirements
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Suggests GEOquery, rmarkdown, knitr, BiocManager, testthat
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Package Archives

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

Source Package RegEnrich_1.13.4.tar.gz
Windows Binary RegEnrich_1.13.4.zip
macOS Binary (x86_64) RegEnrich_1.13.4.tgz
macOS Binary (arm64) RegEnrich_1.13.4.tgz
Source Repository git clone https://git.bioconductor.org/packages/RegEnrich
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RegEnrich
Bioc Package Browser https://code.bioconductor.org/browse/RegEnrich/
Package Short Url https://bioconductor.org/packages/RegEnrich/
Package Downloads Report Download Stats