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pymc-devs / pymc-examples

Examples of PyMC models, including a library of Jupyter notebooks.
https://www.pymc.io/projects/examples/en/latest/
MIT License
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'Tumoroscope' model in PyMC #441

Open jhrcook opened 1 year ago

jhrcook commented 1 year ago

Notebook proposal

'Tumoroscope' model in PyMC

Why should this notebook be added to pymc-examples?

The 'Tumoroscope' model is a generative, graphical model for estimating proportions of cancer sub-clones in spatial transcriptomics data. It was originally built and sampled using a custom Gibbs Sampling process, but I have re-created it in PyMC and used the built-in "Inference Button" to perform sampling.

I would like to contribute this example as a case study to the PyMC gallery, adapting a notebook I have already built.

Suggested categories:

Related notebooks

This is a completely new notebooks proposed as a case study.

References

'Tumoroscope' preprint: https://www.biorxiv.org/content/10.1101/2022.09.22.508914v1 Repository where I have built the model in PyMC: https://github.com/jhrcook/pymc-tumoroscope

ricardoV94 commented 1 year ago

Go for it ;)

drbenvincent commented 1 year ago

Just checking in to see if there was any progress on this? Can always to a draft PR to get comments and feedback on any pain points.

jhrcook commented 1 year ago

Sorry for the delay, but yes I'm still working on it (though slower than I'd like). I have the model, but the description is what takes the most effort.