sc-doublet-detection

name	sc-doublet-detection
description	Annotate putative doublets in single-cell RNA-seq data using Scrublet, DoubletDetection, DoubletFinder, scDblFinder, or scds. The wrapper preserves the current AnnData matrix semantics, standardizes output columns in `obs`, and exports a reusable figure/table gallery.
version	0.6.0
author	OmicsClaw
license	MIT
tags	["singlecell","doublet","scrublet","doubletdetection","doubletfinder","scdblfinder","scds","qc"]
metadata	{"omicsclaw":{"domain":"singlecell","allowed_extra_flags":["--method","--expected-doublet-rate","--threshold","--batch-key","--doubletdetection-n-iters","--doubletdetection-standard-scaling","--no-doubletdetection-standard-scaling","--scds-mode","--r-enhanced"],"param_hints":{"scrublet":"[Truncated]","doubletdetection":"[Truncated]","doubletfinder":"[Truncated]","scdblfinder":"[Truncated]","scds":"[Truncated]"},"legacy_aliases":["sc-doublet"],"saves_h5ad":true,"requires_preprocessed":false}}

Single-Cell Doublet Detection

Why This Exists

• Without it: artificial multiplets can masquerade as transitional or mixed cell states.
• With it: cells receive standardized doublet scores and labels before final clustering, annotation, or DE interpretation.
• Why OmicsClaw: one wrapper harmonizes multiple common backends into the same output columns and gallery layout.

Scope Boundary

Implemented method families:

1. scrublet
2. doubletdetection
3. doubletfinder
4. scdblfinder
5. scds (hybrid, cxds, bcds)

This skill annotates doublets in obs. It does not silently remove cells.

Input Expectations

• Preferred state: raw count-like input in layers["counts"], aligned adata.raw, or count-like adata.X
• Typical stage: after QC review and before final clustering / annotation / DE interpretation
• Important nuance: if the object is already normalized, the wrapper still uses raw counts for calling and preserves the current adata.X semantics

Public Parameters

Shared controls:

• --method
• --expected-doublet-rate

Method-specific controls:

• scrublet
  • --batch-key
  • --threshold
• doubletdetection
  • --doubletdetection-n-iters
  • --doubletdetection-standard-scaling
• scds
  • --scds-mode

Output Contract

Successful runs write:

• processed.h5ad
• report.md
• result.json
• figures/doublet_score_distribution.png
• figures/doublet_call_summary.png
• figures/embedding_doublet_calls.png when an embedding exists or a preview embedding can be computed