RegEnrich

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12

Gene regulator enrichment analysis

Bioconductor version: Development (3.24)

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")):

Weiyang Tao, Aridaman Pandit. RegEnrich: Gene regulator enrichment analysis. doi:10.18129/B9.bioc.RegEnrich, R package version 1.23.2, https://bioconductor.org/packages/RegEnrich.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("RegEnrich")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

No vignettes available
Reference Manual	PDF

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	1.23.2
In Bioconductor since	BioC 3.12 (R-4.0) (6 years)
License	GPL (>= 2)
Depends	R (>= 4.0.0), S4Vectors, dplyr, tibble, BiocSet, SummarizedExperiment
Imports	randomForest, fgsea, enrichit, qvalue, gson, DOSE, BiocParallel, DESeq2, limma, WGCNA, ggplot2 (>= 2.2.0), methods, reshape2, magrittr, BiocStyle
System Requirements
URL

Suggests	GEOquery (>= 2.81.28), rmarkdown, knitr, BiocManager, testthat
Linking To
Enhances
Depends On Me
Imports Me
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Build Report	Build Report, r-universe

Package Archives

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

Source Package
Windows Binary (x86_64)	RegEnrich_1.23.2.zip
macOS Binary (big-sur-x86_64)	RegEnrich_1.23.2.tgz
macOS Binary (sonoma-arm64)	RegEnrich_1.23.2.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