This is a primer for single cell/nuclei ATAC-seq data analysis. What is single cell ATACseq? How do you perform basic scATAC-seq analysis in R? I describe what scATACseq is. Then I use Seurat and Signac to do data analysis using a recent Nature communications paper. I do preprocessing, clustering, differential accessibility analysis, RNA activity estimation, and I make various plots.
Notebook:
https://github.com/mousepixels/sanbomics_scripts/blob/main/scATAC_intro_R.Rmd
References:
https://stuartlab.org/signac/index.html
https://satijalab.org/seurat/articles/get_started.html
https://www.nature.com/articles/s41467-022-30440-2