human-cell-atlas

name	human-cell-atlas
domain	compbio
description	Human Cell Atlas data portal. Use for accessing single-cell reference datasets, cell type markers, and standard atlases.
license	MIT license
metadata	{"skill-author":"Eric Yiru"}

Human Cell Atlas: Reference Atlas

Overview

The Human Cell Atlas (HCA) is a global effort to create a comprehensive reference map of all human cells. The HCA data portal provides access to thousands of single-cell datasets spanning multiple tissues, cell types, and conditions.

When to Use This Skill

This skill should be used when:

• Finding reference single-cell datasets
• Accessing cell type markers and gene expression
• Downloading curated atlases
• Comparing your data to references
• Finding data for specific tissues

Quick Start

Accessing Data

# Using cellxgene-census (for HCA data)
import cellxgene_census

# Get census
census = cellxgene_census.open_soma()

# Query specific tissue
adata = cellxgene_census.get_anndata(
    census,
    organism="Homo sapiens",
    tissue="lung"
)

Direct Download

1. Visit https://data.humancellatlas.org/
2. Browse projects and datasets
3. Download in desired format (h5ad, loom, csv)

Data Portal

Browsing Projects

• Website: https://data.humancellatlas.org/
• Filter by: Tissue, organism, disease, technology
• Metadata: Detailed sample information

Available Data Types

• Single-cell RNA-seq
• Single-cell ATAC-seq
• Spatial transcriptomics
• Multi-omics

Common Uses

Reference Mapping

# Map your data to HCA references
# Use Seurat or scanpy integration

Marker Discovery

# Find markers for cell types
# Query HCA for specific cell types

Additional Resources

• HCA Data Portal: https://data.humancellatlas.org/
• DCP: https://data.humancellatlas.org/explore
• CellxGene Census: https://cellxgene-census.readthedocs.io/