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Companion package to epiregulon with additional plotting, differential and graph functions

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] , Timothy Keyes [aut], Shang-Yang Chen [aut]

Maintainer: Xiaosai Yao <xiaosai.yao at>

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


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

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Data visualization with epiregulon.extra HTML R Script
Reference Manual PDF


biocViews ChipOnChip, DifferentialExpression, GeneExpression, GeneRegulation, GeneTarget, GraphAndNetwork, Network, Normalization, 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 scran, ComplexHeatmap, Matrix, SummarizedExperiment, checkmate, circlize, clusterProfiler, ggplot2, ggraph, igraph, lifecycle, patchwork, reshape2, scales, scater, stats
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Suggests epiregulon, knitr, rmarkdown, parallel, BiocStyle, testthat (>= 3.0.0), EnrichmentBrowser, msigdbr, dorothea, scMultiome, S4Vectors, scuttle, vdiffr, ggrastr, ggrepel
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Follow Installation instructions to use this package in your R session.

Source Package epiregulon.extra_1.0.1.tar.gz
Windows Binary
macOS Binary (x86_64) epiregulon.extra_1.0.1.tgz
macOS Binary (arm64) epiregulon.extra_1.0.1.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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Old Source Packages for BioC 3.19 Source Archive