Skills

A skill is a package of structured files that teaches an AI coding agent how to work with a specific tool or framework. The skill below was generated by Great Docs from this project’s documentation. Install it in your agent and it will be able to run commands, edit configuration, write content, and troubleshoot problems without step-by-step guidance from you.

Any agent — install with npx:

npx skills add https://maayanlab.cloud/Harmonizome/

Codex / OpenCode

Tell the agent:
Fetch the skill file at https://maayanlab.cloud/Harmonizome/skill.md and follow the instructions.

Manual — download the skill file:

curl -O https://maayanlab.cloud/Harmonizome/skill.md

Or browse the SKILL.md file.

SKILL.md

---
name: harmonizome
description: >
  Python wrapper for the Ma'ayan Lab Harmonizome API and dataset downloads. Use when writing Python code that uses the harmonizome package.
license: MIT
compatibility: Requires Python >=3.9.
---

# harmonizome

Python wrapper for the Ma'ayan Lab Harmonizome API and dataset downloads

## Installation

```bash
pip install harmonizome
```

## API overview

### Core API

Public Harmonizome client objects

- `Harmonizome`
- `Entity`

### Harmonizome Methods

Methods for the Harmonizome class

- `Harmonizome.get`
- `Harmonizome.next`
- `Harmonizome.download`
- `Harmonizome.download_df`
- `Harmonizome.get_gene_functional_annotations`
- `Harmonizome.get_gene_with_associations`
- `Harmonizome.download_gene_functional_annotations`
- `Harmonizome.get_gene_associations_summary`
- `Harmonizome.get_gene_functional_associations_formatted`
- `Harmonizome.get_gene_data`

## Resources

- [Full documentation](https://maayanlab.cloud/Harmonizome/)
- [llms.txt](llms.txt) — Indexed API reference for LLMs
- [llms-full.txt](llms-full.txt) — Comprehensive documentation for LLMs
- [Source code](https://github.com/biowrappers/harmonizome)