EpiPack: scATAC-seq integration, reference mapping and cell type annotation
Project description
EpiPack
EpiPack v 0.1.0
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
To-do-list
- Publish to pypi
- Include our own preprocessing functions
- Construct a tutorial website for EpiPack
- Provide pre-trained reference model for all human tissues
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