snATAC pipeline

snATAC pipeline

This repository contains all components of the snATAC-seq pipeline used by the PanKbase Consortium, including Generate position-sorted BAM files using Cell Ranger ATAC, Generate QC Metrics and Chromatin Accessibility Matrices, Window-Based Clustering, Multiplet Detection with AMULET, Removing Multiplets and Reclustering and Peak Based Clustering and cell type annotation