1 Installation

1.1 Installing from github

All the epiregulon components are available on github. There are three separate epiregulon packages. The core epiregulon package supports input in the form of SingleCellExperiment objects. If the users would like to start from ArchR projects, they may choose to use epiregulon.archr package, which allows for the seamless integration with ArchR package through accepting its output to be used in the downstream workflow.

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

# install basic epiregulon package
devtools::install_github(repo='xiaosaiyao/epiregulon')

# install extended version of epiregulon
devtools::install_github(repo='xiaosaiyao/epiregulon.archr')

Moreover, we provide a suite of tools for the enrichment analysis, visualization, and network analysis which can be run on the epireglon or epiregulon.archr output.

# install extended version of epiregulon
devtools::install_github(repo='xiaosaiyao/epiregulon.extra')

The data package scMultiome is for storing TF ChIP-seq data and pre-processed datasets.

# install extended version of epiregulon
devtools::install_github(repo='xiaosaiyao/scMultiome')

1.2 Installing 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")