# Codonfm Score

Validate, prepare, or run public CodonFM Encodon masked-codon variant scoring and...

- Repository: https://github.com/NVIDIA/skills (3812 stars)
- Category: Engineering
- License: Apache-2.0
- Last updated: 2026-10-30
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add NVIDIA/skills --skill codonfm-score -g -a claude-code -y`
Codex: `npx skills add NVIDIA/skills --skill codonfm-score -g -a codex -y`
Cursor: `npx skills add NVIDIA/skills --skill codonfm-score -g -a cursor -y`
Gemini CLI: `npx skills add NVIDIA/skills --skill codonfm-score -g -a gemini-cli -y`
Claude Code plugin marketplace: `/plugin marketplace add NVIDIA/skills`

## Description

Validate, prepare, or run public CodonFM Encodon masked-codon variant scoring and review compatibility of its scoring workflows. Use only when the user explicitly requests CodonFM or Encodon, or that context is already established in the conversation. Do not select this skill for a generic variant-scoring request without that context; ask for the variant and intended analysis first.

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

# Score variants with public Encodon

Run general masked-codon `mutation_prediction` only. This produces a research
signal, not a clinical diagnosis or an expression-direction prediction.

## Instructions

First confirm CodonFM or Encodon context in the user's request or established
conversation. If that context is missing, ask for any missing variant details
and the intended analysis before choosing a model or inspecting model-specific
files. The presence of this skill or source files alone does not establish
the user's intent.

For source reviews and command preparation, inspect the supplied source and
metadata without installing the ML runtime. Use an available Python 3
interpreter with standard-library `zipfile`, `json`, and `csv`; do not assume
the `python` alias or `unzip` exists. Read archive members directly with
`ZipFile.namelist()` and `ZipFile.read()` where possible. If extraction is
needed, use a fresh directory from `tempfile.mkdtemp()` or `mktemp -d` and
preserve existing checkouts and scratch directories. Check whether `rg` is
available; use `grep` or Python if it is absent. Read the source sections
needed for the requested command or compatibility question.

Check whether the request is executable in public v1 before installing or
downloading anything. For synonymous-codon aggregation or Decodon, inspect the
[parser](../../src/runner.py) and [model configuration](../../src/config.py),
explain the missing feature, and finish. Do not implement the missing workflow,
search private code, or keep retrying unsupported commands.

The rest: https://github.com/NVIDIA/skills/blob/HEAD/skills/bionemo-codonfm-score/SKILL.md