epiregulon
This is the development version of epiregulon; for the stable release version, see epiregulon.
Gene regulatory network inference from single cell epigenomic data
Bioconductor version: Development (3.22)
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")):
Wlodarczyk T, Lun A, Wu D, Menon S, Toneyan S, Seidel K, Wang L, Tan J, Chen S, Keyes T, Chlebowski A, Guo Y, Metcalfe C, Hafner M, Siebel CW, Corces MR, Yauch R, Xie S, Yao X (2023). “Epiregulon: Inference of single-cell transcription factor activity to dissect mechanisms of lineage plasticity and drug response.” bioRxiv. doi:10.1101/2023.11.27.568955, https://www.biorxiv.org/content/early/2023/11/28/2023.11.27.568955.
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | 1.5.1 |
| In Bioconductor since | BioC 3.19 (R-4.4) (1 year) |
| 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, beachmat.hdf5 |
| Linking To | Rcpp, beachmat, assorthead |
| 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_1.5.1.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | epiregulon_1.5.0.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 |