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epiregulon

Gene regulatory network inference from single cell epigenomic data


Bioconductor version: Release (3.19)

Gene regulatory networks model the underlying gene regulation hierarchies that drive gene expression and observed phenotypes. Epiregulon infers TF activity in single cells by constructing a gene regulatory network (regulons). This is achieved through integration of scATAC-seq and scRNA-seq data and incorporation of public bulk TF ChIP-seq data. Links between regulatory elements and their target genes are established by computing correlations between chromatin accessibility and gene expressions.

Author: Xiaosai Yao [aut, cre] , Tomasz Włodarczyk [aut] , Aaron Lun [aut], Shang-Yang Chen [aut]

Maintainer: Xiaosai Yao <xiaosai.yao at gmail.com>

Citation (from within R, enter citation("epiregulon")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("epiregulon")

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("epiregulon")
Epiregulon tutorial with MultiAssayExperiment HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews GeneExpression, GeneRegulation, GeneTarget, Network, NetworkInference, SingleCell, Software, Transcription
Version 1.0.1
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.4), SingleCellExperiment
Imports AnnotationHub, BiocParallel, ExperimentHub, Matrix, Rcpp, S4Vectors, SummarizedExperiment, bluster, checkmate, entropy, lifecycle, methods, scran, scuttle, stats, utils, scMultiome, GenomeInfoDb, GenomicRanges, AUCell, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, motifmatchr, IRanges, beachmat
System Requirements
URL https://github.com/xiaosaiyao/epiregulon/
Bug Reports https://github.com/xiaosaiyao/epiregulon/issues
See More
Suggests knitr, rmarkdown, parallel, BiocStyle, testthat (>= 3.0.0), coin, scater
Linking To Rcpp, beachmat
Enhances
Depends On Me
Imports Me
Suggests Me epiregulon.extra
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package epiregulon_1.0.1.tar.gz
Windows Binary epiregulon_1.0.1.zip
macOS Binary (x86_64) epiregulon_1.0.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/epiregulon
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/epiregulon
Bioc Package Browser https://code.bioconductor.org/browse/epiregulon/
Package Short Url https://bioconductor.org/packages/epiregulon/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.19 Source Archive