alterlab-cellxgene
byalterlab-ieu· 90 skills
Query the CZ CELLxGENE Census (61M+ cells) programmatically via cellxgene-census and TileDB-SOMA, slicing expression by tissue, disease, or cell type and returning AnnData. Use when pulling reference single-cell RNA-seq data from the largest curated public atlas, running population-scale queries, or benchmarking your data against a reference — for analyzing your own dataset use scanpy or scvi-tools. Part of the AlterLab Academic Skills suite.
How to install alterlab-cellxgene?
alterlab-ieu/alterlab-academic-skills/alterlab-cellxgene
$npx -y skills add alterlab-ieu/alterlab-academic-skills --skill alterlab-cellxgeneInstalls into the current project.
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Run `npx skills use "https://github.com/alterlab-ieu/alterlab-academic-skills" --skill "alterlab-ieu/alterlab-academic-skills/alterlab-cellxgene"` and follow the generated skill instructions now. Read its complete output, redirecting it to a temporary file first if necessary. Resolve relative paths from the supporting-files directory it provides.
Use the skills in "https://github.com/alterlab-ieu/alterlab-academic-skills" that are relevant to the current task. Run `npx skills add "https://github.com/alterlab-ieu/alterlab-academic-skills"` and select the relevant skills, then follow their instructions.
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