alterlab-cellxgene

What problem does it solve?

Programmatic access to the CZ CELLxGENE Census enables researchers to discover, filter, and analyze millions of single-cell records across thousands of datasets without manual data wrangling.

Core Features & Use Cases

• Metadata exploration: Retrieve cell and dataset metadata with sparse queries to understand available data.
• Expression querying: Load small-to-large expression matrices via get_anndata, axis_query, and related helpers for downstream analyses in Python.
• Machine learning and integration: Train models with PyTorch, and integrate results with Scanpy for end-to-end workflows; multi-dataset integration supports cross-tissue analyses.
• Two-step exploration and query: First explore metadata, then execute targeted queries to retrieve focused cohorts or genes.

Quick Start

Open a census context and execute a basic query to list B cells in lung tissue where is_primary_data is True.