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