status: beta

ScRNA Cell Type Annotator

Automatically annotate cell clusters from scRNA-seq data using marker gene signatures, tissue context, and species-specific references.

Input Validation

This skill accepts: per-cluster marker gene lists from scRNA-seq experiments, with tissue type and species context, for automated cell type annotation.

If the request does not involve scRNA-seq cluster annotation — for example, asking to perform bulk RNA-seq DEG analysis, run clustering from raw counts, or interpret proteomics data — do not proceed. Instead respond:

"scrna-cell-type-annotator is designed to annotate cell clusters from single-cell RNA data using marker genes. Your request appears to be outside this scope. Please provide cluster marker lists with tissue and species context, or use a more appropriate tool for your task. For clustering from raw counts, use Seurat or Scanpy preprocessing pipelines."

When to Use

• Post-clustering annotation of Seurat/Scanpy clusters
• Novel cell type discovery in unexplored tissues
• Cross-study comparison of cell type compositions
• Cell atlas construction and harmonization

Quick Check

python -m py_compile scripts/main.py
python scripts/main.py --help
python scripts/main.py --demo

Workflow

1. Validate input first — confirm the request involves scRNA-seq cluster annotation before any processing. Refuse out-of-scope requests immediately.
2. Confirm objective, required inputs, and constraints before proceeding.
3. Run scripts/main.py with available inputs, or use the documented reasoning path.
4. Return structured result separating assumptions, deliverables, risks, and unresolved items.
5. On execution failure or incomplete inputs, switch to fallback path and state exactly what blocked completion.

Parameters

Parameter	Required	Description
--markers	Yes	DEG marker list per cluster (CSV or JSON)
--tissue	Yes	Organ/tissue context (e.g., "PBMC", "liver")
--species	Yes	"human" or "mouse"
--top-n	No	Top N markers per cluster to use (default: 20)

Marker Database Coverage

The built-in marker database covers 6 PBMC immune cell types (T cells, B cells, NK cells, monocytes, dendritic cells, macrophages). For non-immune or non-PBMC tissues:

• Liver, lung, brain, and other tissue-specific markers are not in the built-in database
• The skill will flag clusters as "novel/unresolved" and provide next-step guidance
• For tissue-specific annotation, provide a custom marker file or reference CellMarker/PanglaoDB

The --tissue and --species parameters are accepted but currently route to the same PBMC-focused database. Tissue-specific routing is a planned enhancement — the script must be updated to load tissue-specific marker dictionaries (e.g., liver, lung, brain) and route based on the --tissue argument.

Path validation: If the --markers path contains ../ or resolves outside the workspace, reject with a path traversal warning and exit with code 1.

Returns

• Cell type predictions per cluster with top supporting markers
• Confidence levels (High / Medium / Low)
• Alternative cell type suggestions where ambiguous
• Clusters flagged as novel or unresolved

Fallback Template

If scripts/main.py cannot run (missing inputs, environment error), respond with:

FALLBACK REPORT
───────────────────────────────────────
Objective      : <stated goal>
Blocked by     : <exact missing input or error>
Partial result : <what can still be assessed manually>
Next step      : <minimum action to unblock>
───────────────────────────────────────

Output Requirements

Every response must make these explicit when relevant:

• Objective or requested deliverable
• Inputs used and assumptions introduced
• Workflow or decision path
• Core result, recommendation, or artifact
• Constraints, risks, caveats, or validation needs
• Unresolved items and next-step checks

Error Handling

• If required inputs are missing, state exactly which fields are missing and request only the minimum additional information.
• If the --markers path contains ../ or resolves outside the workspace, reject with a path traversal warning.
• If the task goes outside documented scope, stop immediately — do not attempt partial analysis before refusing.
• If scripts/main.py fails, report the failure point, summarize what can still be completed safely, and provide the manual fallback above.
• Do not fabricate files, citations, data, search results, or execution outcomes.

Response Template

Use this fixed structure for non-trivial requests:

1. Objective
2. Inputs Received
3. Assumptions
4. Workflow
5. Deliverable
6. Risks and Limits
7. Next Checks

For simple requests, compress the structure but keep assumptions and limits explicit when they affect correctness.

Risk Assessment

Risk Indicator	Assessment	Level
Code Execution	Python scripts executed locally	Medium
Network Access	No external API calls	Low
File System Access	Read marker input, write annotation output	Medium
Data Exposure	Output files saved to workspace	Low

Prerequisites

pip install -r requirements.txt