scanpy
Scanpy
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.
This page mirrors an upstream repository entry. It does not mean the skill is already part of the SCI Skills curated catalog.
- Raw path
- scientific-skills/scanpy
- Allowed tools
- -
- Repository version
- 2.31.0
- Synced at
- March 27, 2026
About this skill
About this skill
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.
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