Metadata-Version: 2.1
Name: pyslingshot
Version: 0.1.3
Summary: Python implementation of the Slingshot pseudotime algorithm
Home-page: https://github.com/mossjacob/pyslingshot
License: MIT
Author: Jacob Moss
Author-email: cob.mossy@gmail.com
Requires-Python: >=3.8,<4.0
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Requires-Dist: anndata
Requires-Dist: matplotlib (>=3.6.0,<4.0.0)
Requires-Dist: networkx
Requires-Dist: notebook
Requires-Dist: numpy (>=1.23.0,<2.0.0)
Requires-Dist: pcurvepy2 (==0.1.5)
Requires-Dist: scikit-learn
Requires-Dist: seaborn (>=0.12.0,<0.13.0)
Requires-Dist: tqdm
Project-URL: Repository, https://github.com/mossjacob/pyslingshot
Description-Content-Type: text/markdown

# 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).


<img src=readme_example.png height="200">

## 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.

