scanpy
bysynthetic-sciences· 59 skills
Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, and visualization. Best for exploratory scRNA-seq analysis with established workflows. For deep learning models use scvi-tools; for data format questions use anndata.
How to install scanpy?
synthetic-sciences/openscience/scanpy
$npx -y skills add synthetic-sciences/openscience --skill scanpyInstalls into the current project.
›Prefer a prompt? Paste this to your agent
Run `npx skills use "https://github.com/synthetic-sciences/openscience" --skill "synthetic-sciences/openscience/scanpy"` 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/synthetic-sciences/openscience" that are relevant to the current task. Run `npx skills add "https://github.com/synthetic-sciences/openscience"` and select the relevant skills, then follow their instructions.
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