# Using the MethScope agent skill

## Overview

The MethScope repository includes an optional agent skill under `agent-skills/methscope/`. The skill gives coding agents project-specific context for MethScope package usage, documentation, `.cg` and `.cm` input files, MRMP embeddings, cell-type prediction, model training, deconvolution, visualization, input conversion, and the `methscope-cli` command-line implementation.

Use the skill when you want an agent to follow the MethScope documentation and repository conventions instead of giving generic methylation-analysis advice.

## Install for Codex

From the root of a cloned `zhou-lab/MethScope` repository, copy the Codex skill entry point and shared MethScope context into your Codex skills directory.

    mkdir -p "$CODEX_HOME/skills/methscope"
    cp agent-skills/methscope/codex/SKILL.md "$CODEX_HOME/skills/methscope/SKILL.md"
    cp -R agent-skills/methscope/core "$CODEX_HOME/skills/methscope/core"

The installed layout should look like this:

    $CODEX_HOME/skills/methscope/
      SKILL.md
      core/
        INSTRUCTIONS.md
        REFERENCES.md
        WORKFLOWS.md

After installation, start a new Codex session or reload the available skills. Then ask Codex to use the MethScope skill for MethScope-specific tasks.

## Example Codex prompts

    Use the MethScope skill to help me test GenerateInput with inst/extdata/example.cg.

    Use the MethScope skill to explain how to convert an ALLC file to a MethScope .cg file.

    Use the MethScope skill to debug a PredictCellType shape mismatch.

    Use the MethScope skill to update the deconvolution tutorial for bundled reference matrices.

## Install for Claude-style project context

For Claude or other agents that use repository-level project instructions, use:

    agent-skills/methscope/claude/CLAUDE.md

If your project already has a `CLAUDE.md`, copy the MethScope-specific guidance from that file into your existing instructions. If your project does not already have one, use `agent-skills/methscope/claude/CLAUDE.md` as the starting project context.

Keep the shared files in `agent-skills/methscope/core/`, because the Claude instructions point to the same package-specific references used by the Codex skill.

## What the skill knows

The shared MethScope skill context includes:

- The difference between GitHub full example data and CRAN toy data
- The role of `.cg`, `.cg.idx`, `.cm`, and bundled reference `.rds` files
- Standard workflows for `GenerateInput()`, `PredictCellType()`, `Input_training()`, `PlotUMAP()`, `PlotConfusion()`, `PlotF1()`, and `nnls_deconv()`
- Guidance for using `example_label.csv` with `.cg.idx` sample order
- Input conversion pointers for BED-like, ALLC, beta/fraction, and binary tracks
- The relationship between the MethScope R package and `methscope-cli`
- `methscope-cli` bundle types: `.ubjx`, `.refx`, and `.updecx`

## Update the skill

When MethScope documentation or package behavior changes, update the source files in:

    agent-skills/methscope/

Then reinstall or recopy the skill into your local agent configuration. The repository copy is the source of truth.