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name: io-data-access description: "Use when working with Scanpy input/output, AnnData persistence, 10x HDF5/MTX ingestion, Visium spatial reads, built-in datasets, annotation queries, sc.get extraction helpers, backed reads, layers, and raw data access." disable-model-invocation: true metadata: disco-role: operating license: BSD 3-Clause

Scanpy IO and Data Access

Use this sub-skill when a task is about getting data into or out of Scanpy, preserving AnnData slots, loading 10x Genomics or Visium outputs, selecting bundled datasets, running annotation/enrichment queries, or extracting values with sc.get.

Route Tasks

• Use references/io-formats.md for sc.read, sc.read_h5ad, sc.read_10x_h5, sc.read_10x_mtx, sc.read_visium, sc.write, adata.write_h5ad, backed mode, layers, raw, and AnnData storage conventions.
• Use references/get-datasets-queries.md for sc.get.obs_df, sc.get.var_df, sc.get.rank_genes_groups_df, sc.get.aggregate, sc.datasets, and sc.queries workflows.
• Use references/troubleshooting.md for missing 10x files, Visium image assets, backed-mode mutation limits, sparse/dense surprises, ambiguous gene keys, dataset downloads, and query dependency/network failures.
• Use scripts/scanpy_io_roundtrip.py to sanity-check an installed Scanpy runtime with a tiny .h5ad roundtrip, layer preservation, backed read inspection, and optional sc.get.obs_df extraction.

Common Decisions

• Prefer sc.read_h5ad(path, backed=None) for normal .h5ad loading; use backed="r" for read-only large-file inspection and backed="r+" only for deliberate backed mutation.
• Prefer sc.read_10x_h5(path, gex_only=True) for Cell Ranger HDF5 feature-barcode matrices; set gex_only=False when antibody, CRISPR, or custom feature rows must be preserved.
• Prefer sc.read_10x_mtx(dir, var_names="gene_symbols", make_unique=True, compressed=True, sparse_format="csr") for Cell Ranger v3+ matrix directories; adjust prefix, compressed=False, or var_names="gene_ids" for nonstandard layouts or uniqueness needs.
• Prefer sc.read_visium(dir, load_images=True) only when Space Ranger spatial assets are available; use load_images=False for counts-only loading. The API is deprecated in current Scanpy releases, so route new spatial workflows to Squidpy when that integration is in scope.
• Prefer sc.write(path, adata) or adata.write_h5ad(path) for persistence; verify .X, .layers, .raw, .obs, .var, .obsm, and .uns fields that downstream steps rely on after roundtrips.

Boundaries

• Do not cover matrix transformations such as filtering, normalization, HVG selection, scaling, batch correction, or QC metric calculation; route those to ../preprocessing-qc/SKILL.md when present.
• Do not cover graph construction, clustering, embeddings, trajectory analysis, or differential-expression computation; route those to ../graph-embedding-analysis/SKILL.md when present.
• Do not cover plotting output, figure export, or report styling; route plotting requests to ../plotting-reporting/SKILL.md when present.
• Do not cover optional external integrations beyond IO/query dependencies; route cross-package integration design to ../external-integrations/SKILL.md when present.