skills/claude-scientific-skills
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Timothy Kassis
2025-10-20 16:19:48 -07:00
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scientific-packages/anndata/SKILL.md
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name: anndata
description: Work with AnnData objects for annotated data matrices, commonly used in single-cell genomics and other scientific domains. This skill should be used when working with .h5ad files, performing single-cell RNA-seq analysis, managing annotated datasets, concatenating multiple datasets, or working with sparse matrices and embeddings in a structured format.
description: Comprehensive AnnData (Annotated Data) manipulation for single-cell genomics, multi-omics, and structured scientific datasets. Use this skill for: loading/saving .h5ad files, creating AnnData objects from matrices/DataFrames, managing obs/var metadata, storing embeddings (PCA/UMAP/t-SNE) in obsm/varm, using layers for raw/normalized data, concatenating datasets with batch tracking, memory-efficient backed mode for large files, sparse matrix optimization, subsetting with views/copies, converting between formats (CSV/MTX/Loom/Zarr), single-cell RNA-seq workflows, batch integration, quality control filtering, dimensionality reduction storage, and scientific data management best practices.
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# AnnData