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 (3.23)
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 "4.6") 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
| Reference Manual |
Details
| biocViews | ChipOnChip, DifferentialExpression, GeneExpression, GeneRegulation, GeneTarget, GraphAndNetwork, Network, Normalization, Software, Transcription |
| Version | 1.7.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (1.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.4), SingleCellExperiment |
| Imports | scran, ComplexHeatmap, Matrix, SummarizedExperiment, checkmate, circlize, clusterProfiler, ggplot2, ggraph, igraph, patchwork, reshape2, scales, scater |
| 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), msigdb, GSEABase, 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 | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/epiregulon.extra |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/epiregulon.extra |
| Package Short Url | https://bioconductor.org/packages/epiregulon.extra/ |
| Package Downloads Report | Download Stats |