single cell Hi-C embedding


scHiCEmbed is a bin-specific embedding method for single-cell Hi-C contact matrices. It uses graph auto-encoders for embedding raw or scHiCluster-imputed single-cell Hi-C matrices. The embedding/latent matrices are used to model 3D genome and detect topologically associating domains (TADs) of individual cells.


scHiCEmbed package can be downloaded here (24M).


  1. Tong Liu and Zheng Wang. scHiCEmbed: Bin-Specific Embeddings of Single-Cell Hi-C Data Using Graph Auto-Encoders. Genes, 2022, 13(6):1048.


For any questions or suggestions, please contact:
Dr. Zheng Wang
Department of Computer Science
University of Miami