Comprehensive Guide to Downstream Analysis for Single-Cell ATAC-Seq in R - scATAC-Seq Workflow

Explore a comprehensive tutorial on downstream analysis of single-cell ATAC-Seq data using R and the Signac package. Learn to annotate cells by integrating scATAC-Seq with scRNA-Seq data, perform differential accessibility analysis, and visualize genomic regions of interest. Follow along with pre-processed 10X Genomics datasets as you create gene activity matrices, transfer cell labels, and develop an interactive genomic browser. Gain insights into strategies for cell annotation and discover useful resources for further exploration of single-cell sequencing analysis techniques.

Intro
scATAC-Seq Analysis Workflow
Strategies to annotate scATAC-Seq cells
Dataset and requirements for demonstration
Starting with pre-processed scATAC-Seq
What is a gene activity matrix?
Creating a gene activity matrix
Visualizing gene activity of canonical markers
Visualizing cell annotations in scRNA-Seq
Integrating scATAC-Seq with scRNA-Seq
Transfer labels from scRNA-Seq to scATAC-Seq
Visualizing scATAC-Seq after integration
Performing differential accessibility analysis
Extracting fold changes for differentially accessible regions
Visualizing genomic regions of interest
Create interactive shiny genomic browser to visualize regions of interest