Research Object Crate for Differential peak analysis with SnapATAC2

Original URL: https://workflowhub.eu/workflows/1089/ro_crate?version=1

This workflow takes a cell-type-annotated AnnData object (processed with SnapATAC2) and performs peak calling with MACS3 on the cell types. Next, a cell-by-peak matrix is constructed and differential accessibility tests are performed for comparison of either two cell types or one cell type with a background of all other cells. Lastly, differentially accessible marker regions for each cell type are identified.

Author
Timon Schlegel
License
CC-BY-4.0

Contents

Main Workflow: Differential peak analysis with SnapATAC2
Size: 24746 bytes