epiregulon.extra

This is the development version of epiregulon.extra; for the stable release version, see epiregulon.extra.

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

Bioconductor version: Development (3.21)

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] (ORCID: ), Tomasz Włodarczyk [aut] (ORCID: ), Timothy Keyes [aut], Shang-Yang Chen [aut]

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

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

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.extra")

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.extra")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ChipOnChip, DifferentialExpression, GeneExpression, GeneRegulation, GeneTarget, GraphAndNetwork, Network, Normalization, Software, Transcription
Version	1.3.0
In Bioconductor since	BioC 3.19 (R-4.4) (0.5 years)
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
System Requirements
URL	https://github.com/xiaosaiyao/epiregulon.extra/
Bug Reports	https://github.com/xiaosaiyao/epiregulon.extra/issues

Suggests	epiregulon, knitr, rmarkdown, parallel, BiocStyle, testthat (>= 3.0.0), EnrichmentBrowser, msigdbr, dorothea, scMultiome, S4Vectors, scuttle, vdiffr, ggrastr, ggrepel
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	epiregulon.extra_1.3.0.tar.gz
Windows Binary (x86_64)	epiregulon.extra_1.3.0.zip (64-bit only)
macOS Binary (x86_64)	epiregulon.extra_1.3.0.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/epiregulon.extra
Source Repository (Developer Access)	git clone [email protected]:packages/epiregulon.extra
Bioc Package Browser	https://code.bioconductor.org/browse/epiregulon.extra/
Package Short Url	https://bioconductor.org/packages/epiregulon.extra/
Package Downloads Report	Download Stats