Complete scanpy scRNA-seq workflow: QC, normalization, HVG, PCA, UMAP, Leiden clustering, and marker gene detection.
/plugin marketplace add Pavel-Kravchenko/Bioinformatics
The exact command may vary by repository. Check the README on GitHub.
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| Step | Function | Key Parameters |
|---|---|---|
| Load data | sc.read_*() | File format |
| QC metrics | sc.pp.calculate_qc_metrics() | qc_vars=['mt'] |
| Filter cells | sc.pp.filter_cells() | min_genes, max_genes |
| Filter genes | sc.pp.filter_genes() | min_cells |
| Normalize | sc.pp.normalize_total() | target_sum=1e4 |
| Log transform | sc.pp.log1p() | — |
| Find HVGs | `sc.pp.hi |
[Description truncada. Veja o README completo no GitHub.]
