scanpyUse for Scanpy single-cell analysis workflows: AnnData IO, preprocessing/QC, graph embeddings, clustering, marker genes, plotting/reporting, optional integrations, and Scanpy package troubleshooting.
Independent GitHub snapshot · Automated classification · Original documentation governs
Use this skill when a task names Scanpy, scanpy, scverse single-cell analysis, AnnData-based analysis, or Scanpy APIs such as sc.pp, sc.tl, sc.pl, sc.get, sc.datasets, sc.queries, sc.metrics, or sc.external.
Scanpy is a Python toolkit for single-cell gene-expression analysis built around anndata.AnnData. It covers data access, preprocessing, quality control, graph construction, dimensionality reduction, clustering, trajectory inference, marker-gene testing, and visualization.
import scanpy as sc.>=3.12.pip install scanpy or conda install -c conda-forge scanpy.pip install 'scanpy[leiden]' or conda install -c conda-forge scanpy python-igraph leidenalg.python -c "import scanpy as sc; print(sc.__version__)".python -m scanpy --help; Scanpy's built-in CLI is intentionally small and primarily exposes settings, while broader ecosystem commands may live in separate packages.Read references/troubleshooting.md before recommending broad dependency changes. Install only the optional extra or package needed by the requested method.
| User need | Route |
|---|---|
Read/write .h5ad, 10x HDF5/MTX, Visium output, backed data, built-in datasets, annotation queries, or extract values from AnnData | sub-skills/io-data-access/SKILL.md |
| Filter cells/genes, compute QC, normalize/log transform, select HVGs, scale/regress, run PCA prep, detect doublets, or manage raw/layer/inplace behavior | sub-skills/preprocessing-qc/SKILL.md |
| Build neighbor graphs, run UMAP/t-SNE/diffmap/draw_graph, cluster with Leiden/Louvain, PAGA/DPT trajectories, marker ranking, gene scoring, ingest, or graph metrics | sub-skills/graph-embedding-analysis/SKILL.md |
| Produce Scanpy plots, save figures headlessly, customize dot/matrix/violin/embedding/spatial plots, or debug color/layout/Matplotlib settings | sub-skills/plotting-reporting/SKILL.md |
Choose optional extras, use scanpy.external, diagnose missing optional dependencies, Dask-backed arrays, or RAPIDS/GPU handoffs | sub-skills/external-integrations/SKILL.md |
io-data-access to load data into an AnnData object and preserve important obs, var, layers, .raw, .obsm, .obsp, and .uns fields.preprocessing-qc for QC, filtering, normalization, HVG selection, scaling/regression, PCA, and other matrix transformations.graph-embedding-analysis after preprocessing to build neighbors and compute embeddings, clusters, trajectories, markers, scores, and graph metrics.plotting-reporting after the relevant annotations exist; plotting functions usually expect keys in .obs, .var, .obsm, .uns, .raw, or .layers created by earlier steps.external-integrations whenever a method requires optional packages, Dask support, RAPIDS/GPU acceleration, or external wrappers.adata.layers["counts"]; use .raw deliberately for downstream marker plotting or differential expression.scanpy.pp, scanpy.tl, scanpy.pl, scanpy.get, scanpy.datasets, scanpy.queries, scanpy.metrics, and scanpy.external.inplace, copy, layer, use_raw, neighbors_key, key_added, and output keys before debugging missing results.leiden, louvain, skmisc, scrublet, scanorama, magic, dask, or plotting only when the workflow needs them.scripts/run_scanpy_skill_smokes.py or the nearest sub-skill smoke script instead of broad upstream test suites.references/repo-provenance.md records the source snapshot and evidence paths used to create this skill; read it before deciding whether a checkout needs refresh.references/troubleshooting.md covers shared install/import, optional dependency, AnnData state, and workflow-routing failures.scripts/run_scanpy_skill_smokes.py runs the safe bundled smoke scripts in the current Python environment.