pymc-devs / pymc-devs/pymc-examples
'Tumoroscope' model in PyMC
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 398
- Forks
- 325
- Avg merge
- 9d 15m
- Merged PRs (30d)
- 1
Description
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:
- Level: Case study
- Diataxis type: Reference
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
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Review the existing PyMC implementation in the linked pymc-tumoroscope repository, then compare it with the case-study notebooks already in pymc-examples. Adapt the existing model into a gallery notebook, following the repository's notebook conventions and the referenced Tumoroscope preprint; done means the new example is complete and suitable for the PyMC gallery.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, python
- Domain
- documentation
- Issue type
- Documentation
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100