epipackpy 0.1.0.dev15

EpiPack: scATAC-seq integration, reference mapping and cell type annotation

EpiPack

EpiPack v 0.1.0dev6

Description

EpiPack is single-cell ATAC-seq atlas construction (integration) and cell type annotation tool. Leveraging its heterogeneous domain adaptation framework, EpiPack is able to

• Integrate multi-source scATAC-seq datasets without aligned peak set
• reference mapping of query datasets
• cell type annotation including OOR detection

Dependency

    python >= 3.8
    pytorch >= 1.11.0
    sklearn >= 0.22.1
    numpy >= 1.21.6
    pandas >= 1.3.5

Note: For pytorch installation, we recommend users go to the pytorch portal to download based on their CUDA version.

Installation

The package has been uploaded to PyPI. Users can download the package and dependent packages by:

    pip install epipackpy

Tutorial

Please checkout the documentations and tutorials at epipack.readthedocs.io.