HTAN Skill for Claude Code

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.

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What It Does

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

Install (Users)

1. Add the plugin to Claude Code

# From the marketplace
/plugin marketplace add ncihtan/htan-claude
/plugin install htan@htan-claude

2. Set up and go

Invoke the skill with /htan. On first use, Claude will:

Create a venv in your project and install the htan CLI from the plugin
Run uv run htan init to 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?"

Demo Outputs

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

Develop (Contributors)

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 .

Authentication

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.

CLI Reference

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 check

All commands accept --help for full usage.

htan

Popularity

What's Inside

README

HTAN Skill for Claude Code

What It Does

Install (Users)

1. Add the plugin to Claude Code

2. Set up and go

Demo Outputs

Develop (Contributors)

Authentication

CLI Reference

Architecture

Confidence

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