A Claude Code plugin for working with the Human Tumor Atlas Network (HTAN) — an NCI Cancer Moonshot initiative constructing 3D atlases of the dynamic cellular, morphological, and molecular features of human cancers as they evolve from precancerous lesions to advanced disease.
| Capability | Auth Required | Description |
|---|---|---|
| Portal queries (ClickHouse) | Synapse team membership | Query file metadata, clinical data, download coordinates |
| Data model | None | Query HTAN data model components, attributes, controlled vocabularies |
| PubMed search | None | Search HTAN-affiliated publications by keyword, author, year |
| File mapping | None | Resolve HTAN file IDs to Synapse/Gen3 download coordinates |
| Synapse download | Synapse token | Download open-access data (processed matrices, clinical) |
| Gen3/CRDC download | Gen3 credentials + dbGaP | Download controlled-access data (raw sequencing) |
| BigQuery metadata | Google Cloud ADC | Query HTAN metadata tables in ISB-CGC |
# From the marketplace
/plugin marketplace add ncihtan/htan-claude
/plugin install htan@htan-claudeInvoke the skill with /htan. On first use, Claude will:
- Create a venv in your project and install the
htanCLI from the plugin - Run
uv run htan initto configure credentials - Suggest adding
Bash(uv run htan *)to your project permissions for smooth usage
Then just ask:
"List all scRNA-seq files from breast cancer in HTAN"
"Search HTAN publications about spatial transcriptomics"
"What attributes are required for scRNA-seq Level 1 manifests?"
Example outputs from running the skill headlessly via claude -p:
| Prompt | Output |
|---|---|
| Give me an overview of what data is available in HTAN | 01_overview.md |
| Find the 10 smallest open-access scRNA-seq breast files | 02_scrna-breast.md |
| What clinical demographics are available for HTAN OHSU? | 03_demographics-ohsu.md |
| Participants per cancer type with both scRNA-seq and imaging (BigQuery) | 04_bigquery-multimodal.md |
| HTAN publications about spatial transcriptomics from 2024 | 05_pubs-spatial.md |
| Required attributes for scRNA-seq Level 1 manifest | 06_model-scrna.md |
| Download the smallest open-access scRNA-seq breast file | 07_download-open.md |
| Download a controlled-access file via Gen3 (dry run) | 08_download-controlled.md |
Re-run with: bash demo/run_demo.sh demo/output
git clone https://github.com/ncihtan/htan-claude.git
cd htan-claude
uv venv && uv pip install -e ".[dev]"
uv run pytest tests/ # 168 tests
# Use as a local plugin
claude --plugin-dir .| Service | How to Set Up |
|---|---|
| Portal | Join HTAN Claude Skill Users team, then run uv run htan init |
| Synapse | Get a Personal Access Token from synapse.org, set SYNAPSE_AUTH_TOKEN or configure ~/.synapseConfig |
| Gen3/CRDC | Request dbGaP access for study phs002371, download credentials from the CRDC portal |
| BigQuery | Run gcloud auth application-default login and set GOOGLE_CLOUD_PROJECT |
See skills/htan/references/authentication_guide.md for detailed instructions.
The htan command is the single interface — used by Claude (via uv run) and by you directly.
uv run htan query portal files --organ Breast --assay "scRNA-seq" --limit 20
uv run htan query portal sql "SELECT atlas_name, COUNT(*) as n FROM files GROUP BY atlas_name"
uv run htan pubs search --keyword "spatial transcriptomics"
uv run htan model components
uv run htan files lookup HTA9_1_19512
uv run htan query bq tables
uv run htan config checkAll commands accept --help for full usage.
htan-claude/
├── src/htan/ # pip-installable package (all deps included)
│ ├── cli.py # Unified CLI: `htan <command>`
│ ├── config.py # Credential management
│ ├── query/portal.py # Portal ClickHouse queries
│ ├── query/bq.py # BigQuery queries
│ ├── download/synapse.py # Synapse downloads
│ ├── download/gen3.py # Gen3/CRDC downloads
│ ├── pubs.py # PubMed search
│ ├── model.py # HTAN data model queries
│ └── files.py # File ID mapping
├── skills/htan/
│ ├── SKILL.md # Skill definition (teaches Claude the CLI)
│ └── references/ # Reference docs (schema, auth, atlases)
├── .claude-plugin/plugin.json # Plugin metadata
├── pyproject.toml # Package definition
└── CLAUDE.md # Developer instructions
No MCP server. The skill teaches Claude the CLI commands. Claude runs them via uv run with blanket Bash(uv run htan *) permission.
MIT