Organize single-cell expression matrices with annotations in AnnData objects.
npx skills add https://github.com/Hung-3008/agusta --skill anndata-hung-3008
Please help me install this Agent Skill. Skill: anndata Source: https://github.com/Hung-3008/agusta/tree/main/.agents/skills/anndata Command: npx skills add https://github.com/Hung-3008/agusta --skill anndata-hung-3008
AnnData provides a compact, flexible data structure to store a gene expression matrix X together with rich annotations (obs, var, layers, obsm, varm, uns) for single-cell experiments, enabling seamless integration and scalable analysis.
Create and manipulate AnnData objects to organize your single-cell experiments and metadata.
High-intent search queries and answers about installing and using this skill.
AnnData organizes scRNA-seq expression matrices by linking matrix X with obs, var, layers, and embeddings in a unified object, enabling seamless integration and scalable analysis for single-cell experiments.
Reading and writing h5ad files is handled by AnnData objects, which support common formats including zarr to perform concatenation, subsetting, and manipulation across preprocessing, clustering, and visualization pipelines.
Backed storage is supported for large scRNA-seq datasets, providing memory-efficient storage options that keep memory usage low while maintaining robust metadata management and validation.
AnnData integrates with Scanpy and the broader scverse ecosystem, allowing you to apply annotated data objects directly in preprocessing, clustering, and visualization workflows.
Concatenating and subsetting annotated single-cell data is performed within the AnnData object, supporting manipulation across formats such as h5ad and zarr to merge multiple experiments.
A unified annotated data structure links the expression matrix X with rich annotations like obs, var, layers, and uns, solving the problem of scattered metadata and ensuring robust ecosystem compatibility.
PharMolixLoad spatial transcriptomics platform outputs into unified AnnData or SpatialData objects.
biomaps-infraManage annotated data matrices for biological and single-cell analysis workflows.
LogauaEngstromCreate and manipulate annotated single-cell omics data matrices in Python.
Zeyuyang-0420Automate single-cell RNA-seq analysis with scvi-tools deep generative models.
