Organize annotated single-cell data with a flexible AnnData structure.
npx skills add https://github.com/mkurman/tamux --skill anndata-mkurman
Please help me install this Agent Skill. Skill: anndata Source: https://github.com/mkurman/tamux/tree/main/skills/scientific-skills/anndata Command: npx skills add https://github.com/mkurman/tamux --skill anndata-mkurman
AnnData provides a flexible, memory-efficient framework for storing a data matrix X alongside rich metadata (obs, var, layers, obsm, varm, uns) to support scalable single-cell analysis workflows.
Create an AnnData object from a small dataset, then progressively attach metadata and embeddings, and persist to disk.
High-intent search queries and answers about installing and using this skill.
AnnData organizes scRNA-seq data matrices alongside aligned annotations like obs, var, layers, and uns, providing a memory-efficient framework for single-cell analysis workflows.
Backed mode enables handling large-scale single-cell datasets larger than memory by efficiently reading and writing dense or sparse data formats like h5ad and zarr.
AnnData offers built-in interoperability with Scanpy, Muon, and the broader scverse ecosystem, supporting preprocessing, visualization, and modeling for scRNA-seq workflows.
Constructing and filtering annotated matrices for omics data uses a flexible structure with core components X, obs, and var, allowing progressive attachment of metadata and embeddings.
Supported I/O formats for single-cell data include h5ad, zarr, MTX, and CSV, accommodating both dense and sparse data structures for scalable analysis.
A dedicated single-cell structure aligns a data matrix X with multi-dimensional metadata like obsm and varm, which standard dataframes cannot natively support for omics workflows.
Lord1EgyptRun variational inference on annotated single-cell omics data matrices with scvi-tools.
TianGzlabLoad, quality control, normalize, and preprocess spatial transcriptomics data into a standardized AnnData object.
tony-zhelonkinRun end-to-end multimodal single-cell RNA+ATAC analysis with Python tools.
OwnLabAIOrganize single-cell data matrices with metadata into AnnData objects.
