RegEnrich

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see RegEnrich.

Gene regulator enrichment analysis

Bioconductor version: 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")
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DifferentialExpression, FunctionalPrediction, GeneExpression, GeneSetEnrichment, GeneTarget, Network, NetworkEnrichment, NetworkInference, RNASeq, Software, Transcription, Transcriptomics, TwoChannel

Version 1.14.0

In Bioconductor since BioC 3.12 (R-4.0) (4 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

URL

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_1.14.0.tar.gz

Windows Binary (x86_64) RegEnrich_1.14.0.zip

macOS Binary (x86_64) RegEnrich_1.14.0.tgz

macOS Binary (arm64) RegEnrich_1.14.0.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/

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