Welcome to EpiPack’s documentation!#

EpiPack is a Python package for end-to-end single-cell ATAC-seq analysis, with core functionalities including reference mapping, cell label transfer, and the detection of out-of-reference (OOR) cell types and states under disease or perturbation conditions.

The package consists of three main components:

  • PEIVI and PEIVI mapping functions for reference construction and query mapping.

  • epk.classifier function for cell label transfer.

  • Global OOR detector and local OOR detector functions for detecting OOR cells under various conditions.

Model architecture

To get started with epipackpy, check out the installation guide and tutorials.