scanpy
Performs Scanpy single-cell RNA-seq QC, normalization, HVG selection, PCA/UMAP/t-SNE, clustering, exploratory marker ranking, pseudobulk preparation, visualization, and Seurat or SingleCellExperiment RDS conversion to h5ad. Applies to established exploratory scRNA-seq workflows with explicit count and expression provenance; complementary skills cover scvi-tools models and AnnData format details.
- Version
- 1.8
- License
- BSD-3-Clause
- Compatibility
- Requires Python 3.12+ and Scanpy; tested with Python 3.13, Scanpy 1.12.4, and AnnData 0.13.4. Optional integrations need separate packages; R conversion needs R. Local analysis needs no credentials or network.
Pinned to revision 68105dd992f1, so it is the text this page describes rather than whatever the author pushed since.
Files
- skills/scanpy/SKILL.md
- skills/scanpy/SKILL_CN.md
- skills/scanpy/assets/analysis_template.py
- skills/scanpy/assets/celltype_mapping.json
- skills/scanpy/assets/gene_signatures.json
- skills/scanpy/assets/pipeline_config.json
- skills/scanpy/references/analysis_workflow.md
- skills/scanpy/references/api_reference.md
- skills/scanpy/references/plotting_guide.md
- skills/scanpy/references/r_interop.md
- skills/scanpy/references/standard_workflow.md
- skills/scanpy/references/upstream-review.md
- skills/scanpy/scripts/_common.py
- skills/scanpy/scripts/annotate.py
- skills/scanpy/scripts/batch_correct.py
- skills/scanpy/scripts/cluster.py
- skills/scanpy/scripts/convert.py
- skills/scanpy/scripts/find_markers.py
- skills/scanpy/scripts/inspect_data.py
- skills/scanpy/scripts/plot.py
- skills/scanpy/scripts/preprocess.py
- skills/scanpy/scripts/pseudobulk.py
- skills/scanpy/scripts/qc_analysis.py
- skills/scanpy/scripts/reduce_dimensions.py
- skills/scanpy/scripts/run_pipeline.py
- skills/scanpy/scripts/score_genes.py
- skills/scanpy/scripts/subset.py
Every link opens the file at its source, pinned to the revision this page describes.