sc-cell-annotation

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.

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Repositorio: mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills-
Última actividad en el origen: 30 de abril de 2026 a las 21:29
Idioma detectado de SKILL.md: inglés
Estrellas: 31
Forks: 8

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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:

manual
markers
celltypist
popv
knnpredict
singler
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

Scenario	Recommended method	Example
PBMC / immune cells (human)	`markers` (default) or `celltypist`	`--method markers`
Immune cells (any tissue, human)	`celltypist`	`--method celltypist --model Immune_All_Low.pkl`
Mouse data	`celltypist` with mouse model, or custom markers	`--method celltypist --model Mouse_Isocortex_Hippocampus.pkl`
Specialized tissue (brain, lung, etc.)	`celltypist` with tissue model, or `--marker-file`	`--method celltypist --model Human_Lung_Atlas.pkl`
Have a labeled reference dataset	`knnpredict` or `popv`	`--method knnpredict --reference ref.h5ad`
R environment available	`singler` or `scmap`	`--method singler --reference HPCA`

Flag	Type	Default	Description	Validation
`--input`	str	—	Input `.h5ad` file	required unless `--demo`
`--output`	str	—	Output directory	required
`--demo`	flag	off	Run with bundled PBMC3k data	—
`--method`	str	`markers`	Annotation method: `manual`, `markers`, `celltypist`, `popv`, `knnpredict`, `singler`, `scmap`	validated against METHOD_REGISTRY
`--model`	str	`Immune_All_Low`	CellTypist model name or file stem	celltypist only
`--reference`	str	`HPCA`	SingleR/scmap atlas key or path to labeled H5AD (popv/knnpredict)	—
`--cluster-key`	str	None	Cluster/label column for marker summaries; auto-detected when omitted	—
`--manual-map`	str	None	Inline cluster-to-label mapping, e.g. `0=T cell;1,2=Myeloid`	manual only
`--manual-map-file`	str	None	Path to mapping file (json/csv/tsv/txt)	manual only
`--marker-file`	str	None	Path to custom marker gene file (JSON or CSV)	markers only
`--celltypist-majority-voting`	flag	off	Enable CellTypist neighborhood majority-voting smoothing	celltypist only
`--species`	str	`Human`	SCSA species filter (`Human`/`Mouse`)	scsa only
`--tissue`	str	`All`	SCSA tissue filter (e.g. `Blood`, `Brain`, `All`)	scsa only
`--scsa-foldchange`	float	1.5	SCSA DE fold-change threshold	scsa only
`--scsa-pvalue`	float	0.05	SCSA DE p-value threshold	scsa only
`--r-enhanced`	flag	off	Also render R Enhanced ggplot2 figures	—

Renderer	Output file	figure_data CSV	Plot description	Required R packages
`plot_embedding_discrete`	`r_embedding_discrete.png`	`annotation_embedding_points.csv`	UMAP/embedding colored by annotated cell types	ggplot2
`plot_embedding_feature`	`r_embedding_feature.png`	`annotation_embedding_points.csv`	UMAP/embedding colored by annotation confidence score	ggplot2
`plot_cell_barplot`	`r_cell_barplot.png`	`cell_type_counts.csv`	Bar chart of cell type counts	ggplot2
`plot_cell_proportion`	`r_cell_proportion.png`	`cell_type_counts.csv`	Stacked proportion bar chart per sample or cluster	ggplot2
`plot_cell_sankey`	`r_cell_sankey.png`	`cluster_annotation_matrix.csv`	Sankey/alluvial diagram from cluster to cell type	ggplot2, ggalluvial

sc-cell-annotation

Opciones de instalación

Revisa los archivos de origen

Single-Cell Cell Annotation

Why This Exists

Scope Boundary

Input Expectations

Public Parameters

Output Contract

Single-Cell Cell Annotation

Why This Exists

Scope Boundary

Input Expectations

Public Parameters

Output Contract

What Users Should Inspect First

Reference Data Guide

Which method should I use?

Custom marker file format

CellTypist models

Reference H5AD for knnpredict / popv

Species and gene naming

Guardrails

CLI Parameters

R Enhanced Plots

Workflow Position

sc-cell-annotation

Datos de origen

Opciones de instalación

Revisa los archivos de origen

Más de este repositorio

Single-Cell Cell Annotation

Why This Exists

Scope Boundary

Input Expectations

Public Parameters

Output Contract

Más de este repositorio

Single-Cell Cell Annotation

Why This Exists

Scope Boundary

Input Expectations

Public Parameters

Output Contract

What Users Should Inspect First

Reference Data Guide

Which method should I use?

Custom marker file format

CellTypist models

Reference H5AD for knnpredict / popv

Species and gene naming

Guardrails

CLI Parameters

R Enhanced Plots

Workflow Position