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.
Installation:
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Requires
numpy,scipy,sklearn -
My fork of
pcurvepy(https://github.com/mossjacob/pcurvepy):pip install git+https://github.com/mossjacob/pcurvepy
-
Finally install pyslingshot:
pip install pyslingshot
[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.