Restore scGen batch-removal tutorial#66
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Re-add scgen_batch_removal.ipynb (removed in 4ef5318), updated for the current pertpy API and kang_2018 schema: - use the exposed `pt.tl.Scgen` name - `batch_key="label"`, `labels_key="cell_type"` (the old `batch`/`celltype` columns are gone) - log-normalize and subsample to 4,000 cells / 2,000 HVGs so it runs in ~2 minutes - `accelerator="cpu"` Outputs regenerated with pertpy's scGen, which now reproduces PyTorch scGen. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Restores
scgen_batch_removal.ipynb, which was removed in4ef5318(Nov 2023), and updates it for the current pertpy API andkang_2018schema.What changed vs the old notebook
pt.tl.Scgen(the oldpt.tl.SCGENalias isn't routed bypt.tl).batch_key="label"(ctrl/stim) +labels_key="cell_type"— the oldbatch/celltypecolumns no longer exist inkang_2018..raw.accelerator="cpu"intrain().ISG15(this is PBMC data; the oldINSis a pancreas gene).Why now
pertpy's JAX scGen previously did not reproduce PyTorch scGen (see scverse/pertpy#1028). With that fixed, the batch-removal demo is meaningful again.
Outputs were regenerated by executing the notebook end-to-end (no errors).
Pairs with a pertpy PR that bumps this submodule and adds the notebook to the tutorials gallery.
🤖 Generated with Claude Code