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Using the MethScope agent skill

agent-skill.Rmd

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.