Installation

Installation of RWireX requires R (>= 4.1).

Additionally, it depends on the following packages:

• ArchR (>= 1.0.1)
• SpectralTAD (>= 1.16.1)
• plotgardener (>= 1.6.2)

install.packages("devtools")
install.packages("BiocManager")

BiocManager::install("plotgardener") # only required for plotCoAccessibilityMap functionality

devtools::install_github("GreenleafLab/ArchR", repos = BiocManager::repositories())
ArchR::installExtraPackages()

devtools::install_github("dozmorovlab/SpectralTAD")

Finally, you can install RWireX:

devtools::install_github("RippeLab/RWireX")

You will need additional genome annotations for visualization.

For human hg38 genome:

BiocManager::install("TxDb.Hsapiens.UCSC.hg38.knownGene")
BiocManager::install("org.Hs.eg.db")

For mouse mm10 genome:

BiocManager::install("TxDb.Mmusculus.UCSC.mm10.knownGene")
BiocManager::install("org.Mm.eg.db")