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
| Maintainer | Weiyang Tao <weiyangtao1513@gmail.com> |
| Author | Weiyang Tao [cre, aut], Aridaman Pandit [aut] |
| License | GPL (>= 2) |
| Downloads rank | 371 |
| Source branch | RELEASE_3_23 |
| biocViews | DifferentialExpression, 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