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universal-single-cell-annotator

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A unified interface for annotating single-cell RNA-seq data using Marker Genes, Deep Learning (CellTypist), or LLMs.

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Source SKILL.md: https://github.com/majiayu000/claude-skill-registry/blob/HEAD/skills/data/RNA/SKILL.md

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---name: universal-single-cell-annotator description: A unified interface for annotating single-cell RNA-seq data using Marker Genes, Deep Learning (CellTypist), or LLMs. license: MIT metadata: author: AI Group version: "1.0.0" category: Genomics compatibility:

  • system: Python 3.9+
  • library: scanpy
  • library: celltypist (optional) allowed-tools:
  • run_shell_command
  • read_file

keywords:

  • rna
  • automation
  • biomedical measurable_outcome: execute task with >95% success rate. ---"

Universal Single-Cell Annotator

This skill wraps multiple cell type annotation strategies into a single Python class. It allows agents to flexibly choose between rule-based (markers), data-driven (CellTypist), or reasoning-based (LLM) approaches depending on the context.

When to Use This Skill

  • Initial Analysis: When processing raw AnnData objects.
  • Validation: When cross-referencing automated labels with known markers.
  • Discovery: When identifying rare cell types using LLM reasoning on marker lists.

Core Capabilities

  1. Marker-Based Scoring: Scores cells based on provided gene lists (e.g., "T-cell": ["CD3D", "CD3E"]).
  2. Deep Learning Reference: Wraps celltypist to transfer labels from massive atlases.
  3. LLM Reasoning: Extracts top markers per cluster and constructs prompts for LLM interpretation.

Workflow

  1. Load Data: Ensure data is in AnnData format (standard for Scanpy).
  2. Choose Strategy:
    • Use Markers if you have a known gene panel.
    • Use CellTypist for broad immune/tissue profiling.
    • Use LLM for novel clusters.
  3. Annotate: Run the corresponding method.
  4. Inspect: Check adata.obs for the new annotation columns.

Example Usage

User: "Annotate this dataset looking for T-cells and B-cells."

Agent Action:

from universal_annotator import UniversalAnnotator
import scanpy as sc

adata = sc.read_h5ad('data.h5ad')
annotator = UniversalAnnotator(adata)

markers = {
    'T-cell': ['CD3D', 'CD3E', 'CD8A'],
    'B-cell': ['CD79A', 'MS4A1']
}

annotator.annotate_marker_based(markers)
# Results in adata.obs['predicted_cell_type']