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

Installation requires the packages: devtools, and Bioconductor packages.

1. Install devtools

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

2. Install Bioconductor

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

3. 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.

References

• Article: https://www.nature.com/articles/s41588-021-00790-6
• Github page: https://github.com/GreenleafLab/ArchR

Reference

• Axel Rosendahl Huber