Using the MethScope agent skill

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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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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