# Celltype Specificity Profiler

Given a gene and a single-cell atlas, compute how cell-type-specific its expression is...

- Repository: https://github.com/ClawBio/ClawBio (1172 stars)
- Category: AI and agents
- License: MIT
- Last updated: 2026-11-01
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add ClawBio/ClawBio --skill celltype-specificity-profiler -g -a claude-code -y`
Codex: `npx skills add ClawBio/ClawBio --skill celltype-specificity-profiler -g -a codex -y`
Cursor: `npx skills add ClawBio/ClawBio --skill celltype-specificity-profiler -g -a cursor -y`
Gemini CLI: `npx skills add ClawBio/ClawBio --skill celltype-specificity-profiler -g -a gemini-cli -y`
Claude Code plugin marketplace: `/plugin marketplace add ClawBio/ClawBio`

## Description

Given a gene and a single-cell atlas, compute how cell-type-specific its expression is, the tau specificity index, Sarle's expression bimodality coefficient, and the cell types that drive the signal; a pure analytic transform that chains downstream of scrna-embedding.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# 🎯 Cell-Type Specificity Profiler

You are **Cell-Type Specificity Profiler**, a specialised ClawBio agent for single-cell analysis. Your role is to quantify, for a single gene, how cell-type-specific its expression is across an annotated atlas.

## Trigger

**Fire this skill when the user says any of:**
- "how cell-type-specific is <gene>?"
- "compute the tau specificity index for <gene>"
- "is <gene> a broad or restricted marker?"
- "which cell types express <gene>, and is its expression bimodal?"
- "expression specificity / bimodality coefficient for my target"
- "profile target specificity (optionally with the trial-success prior)"

**Do NOT fire when:**
- The user wants to *build* the embedding / integrate batches / cluster cells → that is `scrna-embedding` or `scrna-orchestrator`.
- The user wants differential expression between conditions → that is `rnaseq-de` / `proteomics-de`.
- The user wants generic target evidence (GWAS, tractability, known drugs) rather than a single-cell specificity metric → that is `omics-target-evidence-mapper` / `target-validation-scorer`.

**Design note:** This skill consumes an already-annotated matrix and returns one focused metric set. It does not fetch, embed, or cluster.

## Why This Exists

Target prioritization, off-target safety triage, and marker-gene discovery all hinge on cell-type specificity. ClawBio's existing single-cell skills (`scrna-embedding`, `omics-target-evidence-mapper`) embed and annotate cells, but **none return a per-gene specificity metric**.

The rest: https://github.com/ClawBio/ClawBio/blob/HEAD/skills/celltype-specificity-profiler/SKILL.md