PyStemFinder¶

PyStemFinder estimates how far single cells have progressed through differentiation from scRNA-seq data. Less differentiated cells vary more in their expression of cell cycle genes than their neighbors do, and stemFinder scores that heterogeneity within each cell’s k-nearest-neighbor neighborhood.

PyStemFinder is a Python port of the R package stemFinder that works on AnnData objects and scanpy neighbor graphs. Its scores match R’s to within floating point precision; Reproducing the R package shows the comparison.

If you use stemFinder, please cite:

Noller K, Cahan P. Cell cycle expression heterogeneity predicts degree of differentiation. Briefings in Bioinformatics 25(6):bbae536 (2024). https://doi.org/10.1093/bib/bbae536