RegEnrich
Gene regulator enrichment analysis
Bioconductor version: 3.23 · Package version: 1.22.1
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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) |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, FunctionalPrediction, GeneExpression, GeneSetEnrichment, GeneTarget, Network, NetworkEnrichment, NetworkInference, RNASeq, Software, Transcription, Transcriptomics, TwoChannel |
| Package Short Url | https://bioconductor.org/packages/RegEnrich/ |
Citation
From within R, enter citation("RegEnrich"):
Weiyang Tao, Aridaman Pandit. RegEnrich: Gene regulator enrichment analysis. doi:10.18129/B9.bioc.RegEnrich, R package version 1.22.1, https://bioconductor.org/packages/RegEnrich.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | RegEnrich_1.22.1.tar.gz |
| Windows binary (x86_64) | RegEnrich_1.22.1.zip |
| macOS binary (arm64) | RegEnrich_1.22.1.tgz |
| macOS binary (x86_64) | RegEnrich_1.22.1.tgz |
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