Add metacell construction + responder-metacell prediction pipeline#17
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WWXkenmo wants to merge 1 commit into
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Add metacell construction + responder-metacell prediction pipeline#17WWXkenmo wants to merge 1 commit into
WWXkenmo wants to merge 1 commit into
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scripts/metacell_responder/: - build_perturbation_metacells.py single-cell h5ad -> SEACells metacell h5ad - process_metacell_dose_to_zarr.py metacell h5ad -> GroupedDistribution zarr - construct_metacells_from_zarr.py single-cell zarr -> metacell zarr (zarr-native) - define_responder_metacells.py metacell zarr -> responder labels (option-3 kNN) - README.md pipeline, usage, env notes Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
xiaotong743
reviewed
Jun 30, 2026
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| n_meta = max(2, n // cells_per_metacell) | ||
| n_comp = min(n_pca, n - 1, emb.shape[1]) | ||
| emb_pca = PCA(n_components=n_comp, random_state=seed).fit_transform(emb) |
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Has to be PCA? Maybe either flag that or just write a function with predefined embeddings, wdyt?
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scripts/metacell_responder/: