tmb-msi-calculator

Tumor mutation burden and microsatellite instability calculation skill for immunotherapy biomarkers

509 stars

Best use case

tmb-msi-calculator is best used when you need a repeatable AI agent workflow instead of a one-off prompt.

Tumor mutation burden and microsatellite instability calculation skill for immunotherapy biomarkers

Teams using tmb-msi-calculator should expect a more consistent output, faster repeated execution, less prompt rewriting.

When to use this skill

You want a reusable workflow that can be run more than once with consistent structure.

When not to use this skill

You only need a quick one-off answer and do not need a reusable workflow.
You cannot install or maintain the underlying files, dependencies, or repository context.

Installation

Claude Code / Cursor / Codex

$curl -o ~/.claude/skills/tmb-msi-calculator/SKILL.md --create-dirs "https://raw.githubusercontent.com/a5c-ai/babysitter/main/library/specializations/domains/science/bioinformatics/skills/tmb-msi-calculator/SKILL.md"

Manual Installation

Download SKILL.md from GitHub
Place it in .claude/skills/tmb-msi-calculator/SKILL.md inside your project
Restart your AI agent — it will auto-discover the skill

How tmb-msi-calculator Compares

Feature / Agent	tmb-msi-calculator	Standard Approach
Platform Support	Not specified	Limited / Varies
Context Awareness	High	Baseline
Installation Complexity	Unknown	N/A

Frequently Asked Questions

What does this skill do?

Tumor mutation burden and microsatellite instability calculation skill for immunotherapy biomarkers

Where can I find the source code?

You can find the source code on GitHub using the link provided at the top of the page.

SKILL.md Source

# TMB-MSI Calculator Skill

## Purpose
Calculate tumor mutation burden and microsatellite instability for immunotherapy biomarker assessment.

## Capabilities
- TMB calculation from VCF
- MSI status determination
- Neoantigen prediction
- HLA typing integration
- Biomarker thresholds
- Clinical report generation

## Usage Guidelines
- Calculate TMB with appropriate normalization
- Determine MSI status accurately
- Predict neoantigens for immunotherapy
- Apply clinical thresholds for reporting
- Generate actionable reports
- Document methodology and thresholds

## Dependencies
- TMBcat
- MSIsensor2
- MANTIS

## Process Integration
- Tumor Molecular Profiling (tumor-molecular-profiling)

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