RegEnrich
This is the development version of RegEnrich; for the stable release version, see RegEnrich.
Gene regulator enrichment analysis
Bioconductor version: Development (3.18)
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 <weiyangtao1513 at gmail.com>
citation("RegEnrich")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("RegEnrich")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | DifferentialExpression, FunctionalPrediction, GeneExpression, GeneSetEnrichment, GeneTarget, Network, NetworkEnrichment, NetworkInference, RNASeq, Software, Transcription, Transcriptomics, TwoChannel |
| Version | 1.11.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (3 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 |
| Linking To | |
| Suggests | GEOquery, rmarkdown, knitr, BiocManager, testthat |
| System Requirements | |
| Enhances | |
| URL |
See More
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary | RegEnrich_1.11.0.zip |
| macOS Binary (x86_64) | RegEnrich_1.11.0.tgz |
| macOS Binary (arm64) | |
| 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 |