Cfret pilot analysis

[axiomcura]

This PR prepares the analysis of outputs generated by the buscar pipeline. It introduces three notebooks that together document the full buscar workflow, the generation of aggregate profiles, and the computation of cluster centroids identified by buscar.

These notebooks produce intermediate outputs that enable inspection of how buscar processes the data and derives its scoring. Plots and final figures will be added in a subsequent PR.

Notebooks

• 1.cfret-pilot-buscar-analysis.ipynb: Runs the full buscar pipeline.
• 2.2.generate-aggregate-profiles.ipynb: Generates aggregate profiles at the replicate level and treatment-level consensus.
• 3.generate-centroid.ipynb: Computes a centroid for each cluster identified by the buscar module.

Other changes

• 2.preprocessing.ipynb: Removed drug_x (data cannot be published).
• Updated the clustering parameter grid to allow a broader search of the parameter space.

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[wli51]

LGTM! Great work and happy to see things coming together. I have a question about the centroid generating median aggregation step if you could clarify things a little more it would be great

[axiomcura]

Thanks for your review! @wli51