ArchR: Processing scATAC sequencing data¶

ArchR is a R package used for the analysis of scATAC sequencing data. After processing raw scRNAseq FASTQ files using CellRanger.

Installation requires the packages: devtools, and Bioconductor packages.

if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")

2. Install Bioconductor

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

Install ArchR

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

Alternatively, Seurat is a frequently used R package to analyze both scRNA and scATAC sequencing data.