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Strategies to annotate scATAC-Seq cells
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Classroom Contents
Comprehensive Guide to Downstream Analysis for Single-Cell ATAC-Seq in R - scATAC-Seq Workflow
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- 1 Intro
- 2 scATAC-Seq Analysis Workflow
- 3 Strategies to annotate scATAC-Seq cells
- 4 Dataset and requirements for demonstration
- 5 Starting with pre-processed scATAC-Seq
- 6 What is a gene activity matrix?
- 7 Creating a gene activity matrix
- 8 Visualizing gene activity of canonical markers
- 9 Visualizing cell annotations in scRNA-Seq
- 10 Integrating scATAC-Seq with scRNA-Seq
- 11 Transfer labels from scRNA-Seq to scATAC-Seq
- 12 Visualizing scATAC-Seq after integration
- 13 Performing differential accessibility analysis
- 14 Extracting fold changes for differentially accessible regions
- 15 Visualizing genomic regions of interest
- 16 Create interactive shiny genomic browser to visualize regions of interest
