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("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 | ||
| 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 (x86_64) | epiregulon_1.0.1.zip |
| macOS Binary (x86_64) | epiregulon_1.0.1.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 |