scRNA-seq QC

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Read references/qc-annotation-umap-heuristics.md before picking thresholds, annotation backends, or UMAP feature-selection rules.

Confirm what inputs exist before writing code:

• An AnnData object or equivalent with raw counts preserved.
• Per-sample, per-batch, or per-channel metadata, because QC and doublet detection should respect technical partitions.
• Organism, tissue, assay type, chemistry, and whether the data are whole-cell or single-nucleus.
• Whether a matched cell atlas or label-transfer reference exists for the tissue and species.

Preserve provenance in the output: package versions, thresholds, threshold-justification plots, counts removed or flagged at each filter, annotation backend and reference, marker-gene selection heuristic, and any manual cluster exclusions.

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