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.
- Version
- 1.5
- License
- BSD-3-Clause
Pinned to revision de66e10cd0c8, so it is the text this page describes rather than whatever the author pushed since.
Files
- skills/scanpy/SKILL.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/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.