Single-cell Type Order Parameters: identifying cell phenotype from gene expression data

A package for finding projections onto known cell phenotyes, given matrices of raw RNA count data. The theoretical background for this project can be found in Epigenetic Landscapes Explain Partially Reprogrammed Cells and Identify Key Reprogramming Genes by Alex H. Lang, Hu Li, James J. Collins, and Pankaj Mehta.

A manuscript containing the technical details of applying our method to single-cell RNA-seq is in progress, hopefully to be completed Summer 2022.

Sources for reference databases

• Mouse Cell Atlas

• Atlas of Mouse Lung Development

Dependencies

• NumPy

• Pandas

• SciPy