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("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 | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | ChipOnChip, DifferentialExpression, GeneExpression, GeneRegulation, GeneTarget, GraphAndNetwork, Network, Normalization, Software, Transcription |
Version | 1.1.2 |
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 | |
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_1.1.2.tar.gz |
Windows Binary | epiregulon.extra_1.1.2.zip |
macOS Binary (x86_64) | epiregulon.extra_1.1.2.tgz |
macOS Binary (arm64) | epiregulon.extra_1.1.2.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 |