RegEnrich

DOI: 10.18129/B9.bioc.RegEnrich    

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

Gene regulator enrichment analysis

Bioconductor version: Development (3.13)

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>

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

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

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 1.1.0
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
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_1.1.0.tar.gz
Windows Binary RegEnrich_1.1.0.zip
macOS 10.13 (High Sierra) RegEnrich_1.1.0.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

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