RegEnrich
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see RegEnrich.
Gene regulator enrichment analysis
Bioconductor version: 3.13
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 <w.tao-2 at umcutrecht.nl>
citation("RegEnrich")):
Installation
To install this package, start R (version "4.1") 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
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("RegEnrich")| Gene regulator enrichment with RegEnrich | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, FunctionalPrediction, GeneExpression, GeneSetEnrichment, GeneTarget, Network, NetworkEnrichment, NetworkInference, RNASeq, Software, Transcription, Transcriptomics, TwoChannel |
| Version | 1.2.0 |
| 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 | |
| URL |
See More
| Suggests | GEOquery, rmarkdown, knitr, BiocManager, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RegEnrich_1.2.0.tar.gz |
| Windows Binary | RegEnrich_1.2.0.zip |
| macOS 10.13 (High Sierra) | RegEnrich_1.2.0.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/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.13 | Source Archive |