RegEnrich (original) (raw)
This is the released version of RegEnrich; for the devel version, seeRegEnrich.
Gene regulator enrichment analysis
Bioconductor version: Release (3.21)
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
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")
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 | 1.18.1 |
| In Bioconductor since | BioC 3.12 (R-4.0) (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
| 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_1.18.1.tar.gz |
|---|---|
| Windows Binary (x86_64) | RegEnrich_1.18.1.zip |
| macOS Binary (x86_64) | RegEnrich_1.18.1.tgz |
| macOS Binary (arm64) | RegEnrich_1.18.1.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 3.21 | Source Archive |