RegEnrich

DOI: 10.18129/B9.bioc.RegEnrich    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see RegEnrich.

Gene regulator enrichment analysis

Bioconductor version: 3.12

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 <w.tao-2 at umcutrecht.nl>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	DifferentialExpression, FunctionalPrediction, GeneExpression, GeneSetEnrichment, GeneTarget, Network, NetworkEnrichment, NetworkInference, RNASeq, Software, Transcription, Transcriptomics, TwoChannel
Version	1.0.1
In Bioconductor since	BioC 3.12 (R-4.0) (0.5 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
LinkingTo
Suggests	GEOquery, rmarkdown, knitr, BiocManager, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	RegEnrich_1.0.1.tar.gz
Windows Binary	RegEnrich_1.0.1.zip
macOS 10.13 (High Sierra)	RegEnrich_1.0.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RegEnrich
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RegEnrich
Package Short Url	https://bioconductor.org/packages/RegEnrich/
Package Downloads Report	Download Stats