This is a Python implementation of the Slingshot pseudotime algorithm (Street et al., 2018). The original implementation is written in R: https://github.com/kstreet13/slingshot.
A complete working example is located in slingshot.ipynb, using a synthetically generated dataset.
pip install pyslingshot
Older versions if pyslingshot (before v0.1.0) requires manually installing numpy, scipy, sklearn, and my fork
of pcurvepy (https://github.com/mossjacob/pcurvepy).
- Fork & download source
- Install requirements with
poetry install
[1] Street, K., Risso, D., Fletcher, R.B., Das, D., Ngai, J., Yosef, N., Purdom, E. and Dudoit, S., 2018. Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. BMC genomics, 19(1), pp.1-16.