1 Installation

1.1 Install from GitHub

All epiregulon components are available on GitHub. There are three separate packages:
- epiregulon constructs the GRN.
- epiregulon.extra provides tools for visualization, differential TF analysis and network analysis.
- epiregulon.archr provides integration with ArchR.

# install devtools
if(!require(devtools)) install.packages("devtools")

devtools::install_github(repo='xiaosaiyao/epiregulon')
devtools::install_github(repo='xiaosaiyao/epiregulon.extra')
devtools::install_github(repo='xiaosaiyao/epiregulon.archr')

The data package scMultiome stores ChIP-seq data and pre-processed scMultiome datasets.

devtools::install_github(repo='xiaosaiyao/scMultiome')

1.2 Install from Bioconductor

Epiregulon is now available through Bioconductor.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
 
BiocManager::install("epiregulon")
BiocManager::install("epiregulon.extra")
BiocManager::install("scMultiome")