Tangram is a Python package, written in PyTorch and based on scanpy, for mapping single-cell (or single-nucleus) gene expression data onto spatial gene expression data. The single-cell dataset and the spatial dataset should be collected from the same anatomical region/tissue type, ideally from a biological replicate, and need to share a set of genes. Tangram aligns the single-cell data in space by fitting gene expression on the shared genes.

Nature Paper: Biancalani, T., Scalia, G., Buffoni, L. et al. Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram. Nat Methods 18, 1352–1362 (2021). https://doi.org/10.1038/s41592-021-01264-7

Opensource software: https://github.com/broadinstitute/Tangram