> ## Documentation Index
> Fetch the complete documentation index at: https://docs.kalarislabs.com/llms.txt
> Use this file to discover all available pages before exploring further.

# scanpy — AI agent skill for life sciences

> Standard single-cell RNA-seq analysis pipeline.

# `scanpy`

> Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, visualization, and converting R-friendly single-cell formats such as Seurat or SingleCellExperiment RDS files into h5ad for Scanpy. Best for exploratory scRNA-seq analysis with established workflows. For deep learning models use scvi-tools; for data format questions use anndata.

**Category:** [life-sciences](/research-agent-skills/skills#life-sciences) · **License:** BSD-3-Clause · **Version:** 1.6

## Install

```bash theme={null}
npx research-agent-skills install scanpy
npx skills add KalarisLabs/research-agent-skills --skill scanpy
```

## When to use it

Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, visualization, and converting R-friendly single-cell formats such as Seurat or SingleCellExperiment RDS files into h5ad for Scanpy. Best for exploratory scRNA-seq analysis with established workflows. For deep learning models use scvi-tools; for data format questions use anndata.

## Full playbook

Read [SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/main/skills/scanpy/SKILL.md) for the complete workflow, references and any scripts. The agent installer copies the full skill folder.


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