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Cellagent annotation

Skill FridrichMethod/awesome-skills/skills/cellagent-annotation

Cell taggerFrom its SKILL.md

Install
npx -y skills add FridrichMethod/awesome-skills --skill cellagent-annotation

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SKILL.md

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<!-- # COPYRIGHT NOTICE # This file is part of the "Universal Biomedical Skills" project. # Copyright (c) 2026 MD BABU MIA, PhD <[email protected]> # All Rights Reserved. # # This code is proprietary and confidential. # Unauthorized copying of this file, via any medium is strictly prohibited. # # Provenance: Authenticated by MD BABU MIA -->

CellAgent Annotation

Use CellTypeAgent to interpret marker genes, annotate scRNA-seq clusters, and coordinate multi-agent workflows for downstream analysis.

When to Use

  • Automated annotation of scRNA-seq datasets without manual curation.
  • Multi-step workflows (QC → clustering → annotation → DE analysis).
  • Integrating multiple batches requiring consistent labeling.

Core Capabilities

  1. Planning: Multi-agent planner decomposes analysis goals into steps.
  2. Tool execution: Generates Scanpy/Seurat code and runs it autonomously.
  3. Self-correction: Detects execution errors and retries with fixes.

Workflow

  1. Gather marker lists per cluster, plus species/tissue context and optional atlas references.
  2. Run CellTypeAgent (pip install -r requirements.txt then python repo/main.py --data data.h5ad --goal annotate).
  3. Review outputs for supporting markers; downgrade ambiguous clusters when signals conflict.
  4. Produce final table (cluster, label, confidence, supporting markers, notes) and cite references when used.

Example Usage

python3 Skills/Genomics/Single_Cell/CellAgent/repo/main.py --data "./data.h5ad" --goal "annotate"

Guardrails

  • Avoid over-specific lineages if markers overlap; default to broader types.
  • Flag clusters showing multiple signatures for manual review.
  • Respect species/tissue differences when interpreting markers.

References

  • README + upstream paper (Mao et al., 2025 / arXiv 2407.09811).
<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->

What ships with it: 1 file

1.5 KB alongside SKILL.md

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