Reran CFReT dataset with Buscar update

[axiomcura]

This PR reruns the CFReT dataset with the updated Buscar implementation in #74

Note: Once #74 is merged, I will update this branch

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Pull request overview

This PR updates the CFReT analysis notebooks/outputs to align with the redesigned Buscar workflow in #74 (notably removing the clustering/centroid portions), and reruns downstream plotting/analysis artifacts accordingly.

Changes:

• Switch notebook preprocessing to use buscar.preprocess and update the CFReT pilot analysis to use the updated Buscar metrics/signatures workflow (no clustering).
• Add a KS-test + FDR-based “signature importance” analysis and new plotting scripts (PCA comparisons, volcano-style significance plots).
• Update generated notebook artifacts/figures and bump the Ruff pre-commit hook revision.

Reviewed changes

Copilot reviewed 14 out of 33 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
notebooks/2.cfret-analysis/plots/nbconverted/3.cfret-signature-volcano-plot.r	New significance scatter plots (by channel and by on/off signature).
notebooks/2.cfret-analysis/plots/nbconverted/2.sc-agg-consensus-pca-plot.r	New PCA plot comparing single-cell vs aggregate profiles.
notebooks/2.cfret-analysis/plots/nbconverted/1.on-and-off-pca-and-umap-plots.r	Adds clarifying header comments and small formatting/comment tweaks.
notebooks/2.cfret-analysis/plots/figures/well_cluster_heatmap.png	Updated/generated figure artifact.
notebooks/2.cfret-analysis/plots/figures/data_rep_heatmap.png	Updated/generated figure artifact.
notebooks/2.cfret-analysis/plots/figures/data_rep_heatmap.pdf	Updated/generated figure artifact (PDF).
notebooks/2.cfret-analysis/nbconverted/4.generate-pca-umap-components.py	Switch imports to buscar.preprocess for PCA/UMAP.
notebooks/2.cfret-analysis/nbconverted/4.assess-signature-significance.py	New script to compute KS-test + FDR “signature importance” table.
notebooks/2.cfret-analysis/nbconverted/3.generate-pca-umap-components.py	New script to generate PCA/UMAP embeddings for on/off/all feature sets.
notebooks/2.cfret-analysis/nbconverted/3.generate-centroid.py	Removed centroid-generation (clustering workflow no longer used).
notebooks/2.cfret-analysis/nbconverted/1.cfret-pilot-buscar-analysis.py	Update pilot analysis to new Buscar workflow (signatures + phenotypic activity; no clustering).
notebooks/2.cfret-analysis/4.assess-signature-significance.ipynb	New notebook version of the signature significance analysis.
notebooks/2.cfret-analysis/3.generate-pca-umap-components.ipynb	Updated notebook to use buscar.preprocess and refreshed outputs/metadata.
notebooks/2.cfret-analysis/3.generate-centroid.ipynb	Removed centroid notebook (clustering workflow removed).
notebooks/2.cfret-analysis/2.generate-aggregate-profiles.ipynb	Notebook metadata update (Python version change).
notebooks/2.cfret-analysis/1.cfret-pilot-buscar-analysis.ipynb	Updated notebook to use Buscar modules directly; removes clustering steps.
.pre-commit-config.yaml	Bumps Ruff hook revision.

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