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updated readthedocs link
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fra-pcmgf committed Apr 7, 2024
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Expand Up @@ -3,8 +3,11 @@ This package is a Python implementation of GeneTrajectory.
The method is described in detail in the article [
Gene trajectory inference for single-cell data by optimal transport metrics](
https://doi.org/10.1038/s41587-024-02186-3).

Documentation and tutorials are available at https://genetrajectory-python.readthedocs.io
For the R implementation, go to the [GeneTrajectory](https://github.com/KlugerLab/GeneTrajectory) project.


Note that, although the implementation is equivalent, it will produce slightly different results to the R implementation
because the signs of eigenvectors may differ and because of the randomness of K-means during the `coarse_grain` step.

Expand All @@ -21,8 +24,8 @@ pip install git+https://github.com/Klugerlab/GeneTrajectory-python.git
```

# Tutorials #
There are tutorials in Jupyter Notebook format in the
[notebooks](https://github.com/KlugerLab/GeneTrajectory-python/tree/main/notebooks) folder of the GitHub project.
There are tutorials in Jupyter Notebook format in the [online documentation](https://genetrajectory-python.readthedocs.io).
[notebooks](https://github.com/KlugerLab/GeneTrajectory-python/tree/main/docs/notebooks) folder of the GitHub project.
To get started, please follow the tutorial on Human myeloid cells on
[tutorial_human_myeloid.ipynb](https://github.com/KlugerLab/GeneTrajectory-python/blob/main/notebooks/tutorial_human_myeloid.ipynb)

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