Borrowing it
Nothing to install: this file belongs to cafferychen777/ChatSpatial. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.
curl -O https://raw.githubusercontent.com/cafferychen777/ChatSpatial/main/.agents/skills/functional-analysis/SKILL.mdgit clone --depth 1 https://github.com/cafferychen777/ChatSpatialWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/cafferychen777/chatspatial/functional-analysis)<a href="https://agentmods.dev/skills/cafferychen777/chatspatial/functional-analysis"><img src="https://agentmods.dev/badge/skills/cafferychen777/chatspatial/functional-analysis.svg" alt="Measured on agentmods" height="20"></a>- NVIDIA SkillSpector pass
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00087 | $0.01921 |
| Opus 5 | $0.00044 | $0.00960 |
| Sonnet 5 | $0.00017 | $0.00384 |
| Haiku 4.5 | $0.00009 | $0.00192 |
Grade A, and why
functional-analysis scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 8d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 288 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Functional Analysis
Overview
This skill answers: What biological processes/pathways are represented by this gene set?
Two main approaches:
- Over-representation Analysis (ORA): Test if genes are enriched in pathways
- Gene Set Enrichment Analysis (GSEA): Use full ranked gene list
Plus specialized analysis: 3. CNV Analysis: Copy number variation in spatial context (tumor analysis)
Decision Tree: Which Method?
Q: What type of gene list do you have?
│
├─ Discrete gene list (DEGs, markers)
│ └─ Over-Representation Analysis (ORA)
│ ├─ Input: Gene list (up/down regulated)
│ ├─ Tests: Hypergeometric / Fisher's exact
│ └─ Output: Enriched pathways with p-values
│
├─ Ranked gene list (all genes with scores)
│ └─ Gene Set Enrichment Analysis (GSEA)
│ ├─ Input: All genes ranked by fold change/statistic
│ ├─ Tests: Running sum statistic
│ └─ Output: Enrichment scores, leading edge genes
│
└─ Spatial tumor data
└─ CNV Analysis
├─ Infer copy number from expression
├─ Map CNV spatially
└─ Identify subclones
Over-Representation Analysis (ORA)
When to Use
- You have a discrete gene list (e.g., significant DEGs)
- Want to know what pathways are enriched
- Quick, interpretable results needed
Databases
| Database | Content | Best For |
|---|---|---|
| GO (Gene Ontology) | BP, MF, CC terms | Broad functional annotation |
| KEGG | Metabolic/signaling pathways | Pathway diagrams |
| Reactome | Curated pathways | Detailed mechanisms |
| MSigDB | Hallmarks, curated sets | Cancer, immunology |
| WikiPathways | Community pathways | Specific processes |
Workflow
Step 1: Prepare Gene List
Requirements:
- Gene symbols or IDs (consistent naming)
- Typically 50-500 genes works best
- Separate up/down regulated if directional
Step 2: Run ORA
Use analyze_enrichment tool with:
gene_list: Your genes of interestdatabase: "GO_BP", "KEGG", "Reactome", etc.background: All detected genes (important!)
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 8d ago First seen · 288 lines · 87 tokens per session scan A f2f32c605d3f
functional-analysis is a skill published in the GitHub repository cafferychen777/ChatSpatial (44 stars, last pushed 23d ago), licensed MIT. It adds 87 tokens to every session and 1,921 once invoked, about $0.0004 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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