Individual skill
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.
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- single-cell-rna-seq,-scrna-seq,-clustering,-umap,-bioinformatics Declared skill tag
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Read excerpt
# Scanpy: Single-Cell Analysis
## Overview
Scanpy is a scalable Python toolkit for analyzing single-cell RNA-seq data, built on AnnData. Apply this skill for complete single-cell workflows including quality control, normalization, dimensionality reduction, clustering, marker gene identification, visualization, and trajectory analysis. Current stable release: **scanpy 1.12.x** (January 2026).
## Installation
Requires Python **3.12+** (scanpy 1.12 dropped Python ≤3.11) and anndata **≥0.10**.
```bash
uv pip install "scanpy[leiden]"
```
