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RegEnrich

Gene regulator enrichment analysis


Bioconductor version: Release (3.18)

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 "4.3") 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

Reference Manual PDF

Details

biocViews DifferentialExpression, FunctionalPrediction, GeneExpression, GeneSetEnrichment, GeneTarget, Network, NetworkEnrichment, NetworkInference, RNASeq, Software, Transcription, Transcriptomics, TwoChannel
Version 1.12.0
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
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
Windows Binary RegEnrich_1.12.0.zip
macOS Binary (x86_64) RegEnrich_1.12.0.tgz
macOS Binary (arm64) RegEnrich_1.12.0.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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