cellxgene-census
Category: scientific-databases · License: MIT · Version: 1.3
Tags: single-cell, transcriptomics, public datasets, spatial transcriptomics, bioinformatics
When to use it
Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. For analyzing your own local single-cell data use scanpy, anndata, or scvi-tools.Example requests
Ask your agent in plain language, for example:- “How many primary human B cells are in the latest Census LTS release, broken down by tissue?”
- “I’m writing a methods section for a lung fibrosis paper. I need all primary Homo sapiens cells from lung with disease ‘pulmonary fibrosis’ from CELLxGENE, only the columns cell_type, donor_id, dataset_id and assay, plus expression for SFTPC and KRT5, loaded into an AnnData I can pass to scanpy. My laptop has 16 GB RAM and my first attempt with get_anndata crashed with a memory error.”
- “I want to train a cell type classifier on millions of public human brain single-cell profiles without downloading every dataset by hand. What’s the right way to stream that data into PyTorch and keep the training set reproducible?”
Install
/plugin marketplace add KalarisLabs/research-agent-skills and install the whole scientific-databases category with /plugin install scientific-databases@research-agent-skills.