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RegEnrich

Gene regulator enrichment analysis

Bioconductor version: 3.23 · Package version: 1.22.1

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.

Installation

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

BiocManager::install("RegEnrich")

Details

MaintainerWeiyang Tao <weiyangtao1513@gmail.com>
AuthorWeiyang Tao [cre, aut], Aridaman Pandit [aut]
LicenseGPL (>= 2)
Downloads rank371
Source branchRELEASE_3_23
biocViewsDifferentialExpression, FunctionalPrediction, GeneExpression, GeneSetEnrichment, GeneTarget, Network, NetworkEnrichment, NetworkInference, RNASeq, Software, Transcription, Transcriptomics, TwoChannel

Documentation

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Dependencies

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

Suggests: GEOquery, rmarkdown, knitr, BiocManager, testthat