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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 (3.20)

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 gmail.com>

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

Installation

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

Details

biocViews ChipOnChip, DifferentialExpression, GeneExpression, GeneRegulation, GeneTarget, GraphAndNetwork, Network, Normalization, Software, Transcription
Version 1.1.0
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
System Requirements
URL https://github.com/xiaosaiyao/epiregulon.extra/
Bug Reports https://github.com/xiaosaiyao/epiregulon.extra/issues
See More
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
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Links To Me
Build Report Build Report

Package Archives

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

Source Package epiregulon.extra_1.1.0.tar.gz
Windows Binary epiregulon.extra_1.1.0.zip (64-bit only)
macOS Binary (x86_64) epiregulon.extra_1.1.0.tgz
macOS Binary (arm64) epiregulon.extra_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/epiregulon.extra
Source Repository (Developer Access) git clone git@git.bioconductor.org: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