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Intro
What is ATAC-Seq?
Difference between bulk and single cell ATAC-Seq
Applications of scATAC-seq
scATAC-Seq workflow
packages/tools to process scATAC-Seq
Signac vignette and data
What is a fragment file?
What does the cell x feature matrix look like? How different is it from scRNA-Seq?
Creating a ChromatinAssay
Reading in the metadata
Creating a SeuratObject
Add gene annotations to SeuratObject
Understanding quality control for scATAC-Seq
What is Nucleosome Signal and Nucleosome banding pattern?
What is Transcription Start Site (TSS) enrichment score?
Additional QC metrics
Compute QC metric
Visualizing QC
Filter poor quality cells
Normalization and linear dimensionality reduction
Non-linear dimensionality reduction and clustering