scATAnno: An Automated Cell Type annotation Pipeline for scATAC-seq

scATAnno is a Python-based workflow that automates the annotation of single-cell ATAC-seq (scATAC-seq) data using reference atlases. It directly uses chromatin accessibility peaks as input features. scATAnno utilizes large-scale reference atlases constructed from publicly available datasets and various scATAC-seq technologies to annotate cell types in an unsupervised manner. It incorporates uncertainty score metrics to assess the confidence of cell-type assignments. The workflow has been demonstrated to accurately annotate cell types in different case studies, including PBMC, TNBC, and BCC, and can identify unknown cell populations. Overall, scATAnno expedites our understanding of cellular heterogeneity based on chromatin accessibility profiles in complex biological systems.

  • Integration of newly generated scATAC-seq data with reference atlases

  • Celltype annotation of single-cell chromatin accessibility profile

  • Uncertainty score distribution to assess cell-type assignment

Workflow of scATAC Annotation

If you use this pipeline, please cite the following reference:

Jiang et al., scATAnno: Automated Cell Type Annotation for single-cell ATAC-seq Data

BioRxiv Preprint (

The documentation is organized into the following sections: