scATACseq data are very sparse. It is sparser than scRNAseq. To do clustering of scATACseq data, there are some preprocessing steps need to be done.

I want to reproduce what has been done after reading the method section of these two recent scATACseq paper:

  1. A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility Darren et.al Cell 2018
  • Latent Semantic Indexing Cluster Analysis

In order to get an initial sense of the relationship between …