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:
github.com/mousepixels/sanbom...
References:
stuartlab.org/signac/index.html
satijalab.org/seurat/articles...
www.nature.com/articles/s4146...
Негізгі бет Ғылым және технология Introduction to single cell ATAC data analysis in R
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