sc-cell-annotation

name	sc-cell-annotation
description	Annotate cell types from normalized scRNA-seq data using marker scoring, CellTypist, PopV-style reference mapping, lightweight KNNPredict-style mapping, SingleR, or scmap through shared Python/R backends.
version	0.9.0
author	OmicsClaw
license	MIT
tags	["singlecell","annotation","celltypist","popv","knnpredict","singler","scmap"]
metadata	{"omicsclaw":{"domain":"singlecell","allowed_extra_flags":["--manual-map","--manual-map-file","--cluster-key","--method","--model","--reference","--marker-file","--celltypist-majority-voting","--no-celltypist-majority-voting","--r-enhanced"],"param_hints":{"manual":"[Truncated]","markers":"[Truncated]","celltypist":"[Truncated]","popv":"[Truncated]","knnpredict":"[Truncated]","singler":"[Truncated]","scmap":"[Truncated]"},"legacy_aliases":["sc-annotate"],"saves_h5ad":true,"requires_preprocessed":true}}

Single-Cell Cell Annotation

Why This Exists

• Without it: users hand-label clusters inconsistently or trust opaque defaults.
• With it: annotation method, reference/model choice, label outputs, and figures are standardized.
• Why OmicsClaw: one wrapper unifies marker-based and reference-style annotation while preserving an AnnData-first workflow.

Scope Boundary

Implemented methods:

1. manual
2. markers
3. celltypist
4. popv
5. knnpredict
6. singler
7. scmap

This skill annotates cells or clusters. It does not replace marker discovery or replicate-aware DE.

Input Expectations

• Expected state: normalized expression in adata.X
• Typical upstream step: sc-clustering
• Typical downstream steps: sc-markers, sc-de, or interpretation/reporting
• Marker mode needs an existing cluster/label column; it will not auto-cluster anymore

Public Parameters

• --method
• --manual-map
• --manual-map-file
• --cluster-key
• --model
• --reference
• --marker-file
• --celltypist-majority-voting

Output Contract

Successful runs write:

• processed.h5ad
• report.md
• result.json
• figures/embedding_cell_type.png
• figures/embedding_cluster_vs_cell_type.png
• figures/cluster_to_cell_type_heatmap.png
• figures/cell_type_counts.png
• figures/embedding_annotation_score.png when scores are available
• figures/manifest.json
• figure_data/manifest.json
• tables/annotation_summary.csv