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Standard single-cell RNA-seq analysis pipeline.
Passed 21 of 23 test cases with the skill, and 13 of 23 without it.
and 10 more in the full report
9 fixed14 passed either way2 still failing0 broke
Tokens, turns and time describe resource use, not a dollar price.
One of 8 test cases the skill fixed. Same model, same prompt, with and without the skill.
When running feature selection for single-cell data prior to dimensionality reduction, what is the standard recommended default for `n_top_genes` in `sc.pp.highly_variable_genes`?
| Checked | Without skill | With skill |
|---|---|---|
| Specifies setting n_top_genes to 2000. | Passed | Passed |
| Calls sc.pp.highly_variable_genes to perform feature selection. | Missed | Passed |
The instructions your model reads when the skill loads.
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. Current stable release: scanpy 1.12.x (January 2026).
Requires Python 3.12+ (scanpy 1.12 dropped Python ≤3.11) and anndata ≥0.10.
uv pip install "scanpy[leiden]"
The [leiden] extra installs python-igraph and leidenalg, required for Leiden clustering. For reproducible environments, pin a version: uv pip install "scanpy[leiden]==1.12.1".
For large or out-of-core datasets, many functions support Dask arrays (experimental):
uv pip install "scanpy[leiden]" dask
See the Using dask with Scanpy tutorial. For GPU-accelerated scanpy-like operations, use rapids-singlecell as a separate package.
If the input is an R-native single-cell object (.rds, .RData, Seurat, or SingleCellExperiment), first convert it to .h5ad with R tooling, then load it with Scanpy. Read references/r_interop.md for agent-run installation and conversion instructions across macOS, Linux, and Windows.
For AnnData structure and I/O details, use the anndata skill. For probabilistic models and batch correction, use scvi-tools.
This skill should be used when:
.rds, .RData, Seurat, SingleCellExperiment) that need conversion to .h5adtest cases passed, vs 13 / 23 without
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