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Slingshot in Python

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:

• pip install pyslingshot

Deprecated version

Older versions if pyslingshot (before v0.1.0) requires manually installing numpy, scipy, sklearn, and my fork of pcurvepy (https://github.com/mossjacob/pcurvepy).

Contributing

• 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.