How do I install the Clarity Analyze skill?

Run npx skillmds@latest add modbender/clarity-analyze in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Clarity Analyze safe to use?

This skill has not completed SkillMD's automated safety review yet. Independent scanners report: SkillSpector: PASS, Skill Scanner: PASS. Capability flags: executes scripts. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Clarity Analyze?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Clarity Analyze free to use?

Yes. Installing skills from SkillMD is free. This skill is licensed under MIT.

Who published Clarity Analyze?

modbender (@modbender) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Clarity Analyze by modbender — Agent Skill

Name: Clarity Analyze
Rating: 4.5 (4 reviews)
Author: modbender

Clarity Analyze

Submit research questions for AI-powered analysis via Clarity Protocol. Use when the user asks to analyze a protein variant, ask a research question, get AI analysis of a mutation, or query Clarity's aggregated data sources. Requires CLARITY_WRITE_API_KEY. Capabilities: submit analysis questions, get AI answers grounded in 7 data sources.

modbender Updated Sep 9, 2026 12 repo stars

File contents

Clarity Analyze Skill

Submit research questions to Clarity Protocol's AI analysis engine. Questions are answered using data from 7 aggregated sources: fold data, ClinVar, gnomAD, PubMed literature, Open Targets, agent findings, and agent annotations.

Quick Start

Ask a research question:

python scripts/ask_question.py --question "What is the clinical significance of SOD1 A4V?"

Ask about a specific variant:

python scripts/ask_question.py \
  --question "How does this mutation affect protein stability?" \
  --variant-id 1 \
  --focus clinical literature

Get plain text answer (no JSON wrapper):

python scripts/ask_question.py \
  --question "What is the clinical significance of SOD1 A4V?" \
  --format text

Data Sources

The analysis engine draws from:

Fold data — AlphaFold structure predictions, confidence scores
Clinical data — ClinVar pathogenicity, gnomAD allele frequency
Literature — PubMed papers and citations
Structural analysis — AlphaFold structural predictions
Open Targets — Disease-gene associations
Agent findings — Research agent discoveries
Agent annotations — Community observations

Focus Options

Prioritize specific data sources in the analysis:

clinical — ClinVar, gnomAD data
literature — PubMed papers
structural — AlphaFold predictions
functional — Open Targets, agent findings

Authentication

export CLARITY_WRITE_API_KEY=your_write_key_here

Rate Limits

Analysis requests: 10 per day (per API key)
Identical questions return cached responses (7-day TTL)

Error Handling

403 Forbidden: Invalid or missing write API key
404 Not Found: Specified variant does not exist
422 Validation Error: Question is off-topic (must be about protein research)

---name: clarity-analyzedescription: Submit research questions for AI-powered analysis via Clarity Protocol. Use when the user asks to analyze a protein variant, ask a research question, get AI analysis of a mutation, or query Clarity's aggregated data sources. Requires CLARITY_WRITE_API_KEY. Capabilities: submit analysis questions, get AI answers grounded in 7 data sources.license: MIT--- # Clarity Analyze Skill Submit research questions to Clarity Protocol's AI analysis engine. Questions are answered using data from 7 aggregated sources: fold data, ClinVar, gnomAD, PubMed literature, Open Targets, agent findings, and agent annotations. ## Quick Start Ask a research question: ```bash python scripts/ask_question.py --question "What is the clinical significance of SOD1 A4V?" ``` Ask about a specific variant: ```bash python scripts/ask_question.py \ --question "How does this mutation affect protein stability?" \ --variant-id 1 \ --focus clinical literature ``` Get plain text answer (no JSON wrapper): ```bash python scripts/ask_question.py \ --question "What is the clinical significance of SOD1 A4V?" \ --format text ``` ## Data Sources The analysis engine draws from: 1. **Fold data** — AlphaFold structure predictions, confidence scores 2. **Clinical data** — ClinVar pathogenicity, gnomAD allele frequency 3. **Literature** — PubMed papers and citations 4. **Structural analysis** — AlphaFold structural predictions 5. **Open Targets** — Disease-gene associations 6. **Agent findings** — Research agent discoveries 7. **Agent annotations** — Community observations ## Focus Options Prioritize specific data sources in the analysis: - `clinical` — ClinVar, gnomAD data - `literature` — PubMed papers - `structural` — AlphaFold predictions - `functional` — Open Targets, agent findings ## Authentication ```bash export CLARITY_WRITE_API_KEY=your_write_key_here ``` ## Rate Limits - **Analysis requests**: 10 per day (per API key) - Identical questions return cached responses (7-day TTL) ## Error Handling - **403 Forbidden**: Invalid or missing write API key - **404 Not Found**: Specified variant does not exist - **422 Validation Error**: Question is off-topic (must be about protein research)

Frequently asked questions