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name: aucell-and-binarization description: "Score pySCENIC regulon or gene-signature activity with AUCell, derive thresholds, binarize AUC matrices, inspect activity plots, and compute regulon specificity scores." disable-model-invocation: true metadata: disco-role: operating license: GPL 3.0

AUCell And Binarization

Use this sub-skill when the task starts from an expression matrix plus already-created regulons or gene signatures and needs cell-level activity scoring, activity thresholding, binary regulon calls, activity inspection, or RSS summaries.

Route Here

• Run pyscenic aucell or pyscenic.aucell.aucell on CSV/TSV, loom, h5ad, GMT, YAML, DAT, or motif-table-derived signatures.
• Check whether expression input is cells-by-genes, whether text input needs --transpose, and whether AUCell output is cells-by-regulons.
• Choose auc_threshold, seed, num_workers, --weights, noweights, or normalize settings for scoring.
• Use derive_auc_threshold, create_rankings, aucell4r, derive_threshold, binarize, plot_binarization, plot_rss, or regulon_specificity_scores.
• Diagnose empty signatures, non-overlapping gene names, multiprocessing memory behavior, optional loom/h5ad dependency issues, and unimodal threshold results.

Route Elsewhere

• Create modules, motif-prune them, or convert enriched motifs into regulons with ../motif-pruning-and-regulons/SKILL.md.
• Export SCope loom or AnnData metadata beyond AUCell output append behavior with ../data-io-and-export/SKILL.md.
• Build end-to-end grn -> ctx -> aucell CLI/container recipes with ../cli-and-containers/SKILL.md.

Bundled References

• references/api-reference.md lists the AUCell, binarization, plotting, RSS, CLI, and signature-format contracts.
• references/workflows.md gives safe API and CLI recipes for scoring, thresholding, binarization, plotting, RSS, and orientation checks.
• references/troubleshooting.md covers common failures and ambiguous outputs for AUCell and binarization.
• scripts/aucell_smoke.py runs a tiny deterministic AUCell API smoke test and can print equivalent CLI guidance.

Quick Start

python scripts/aucell_smoke.py --show-cli

For real data, keep expression matrices as cells x genes for the Python API and CSV/TSV CLI input unless using pyscenic aucell --transpose for genes x cells text files. Treat returned AUC and binary matrices as cells x regulons.