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Bioconductor - RegEnrich (development version)

RegEnrich

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

Gene regulator enrichment analysis

Bioconductor version: Development (3.22)

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 "4.5") and enter:


if (!require("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")
Details biocViews DifferentialExpression, FunctionalPrediction, GeneExpression, GeneSetEnrichment, GeneTarget, Network, NetworkEnrichment, NetworkInference, RNASeq, Software, Transcription, Transcriptomics, TwoChannel Version 1.19.0 In Bioconductor since BioC 3.12 (R-4.0) (4.5 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, BiocStyle System Requirements URL See More Package Archives

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

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