Create, read, write, and manipulate AnnData objects for single-cell genomics.
npx skills add https://github.com/ovachiever/droid-tings --skill anndata-ovachiever
Please help me install this Agent Skill. Skill: anndata Source: https://github.com/ovachiever/droid-tings/tree/main/skills/anndata Command: npx skills add https://github.com/ovachiever/droid-tings --skill anndata-ovachiever
AnnData provides a robust data structure to store biological measurements, annotations, and multi-dimensional data, enabling scalable analysis workflows with Scanpy and the broader scverse ecosystem.
Use cases include single-cell analysis, multi-omics integration, and large-scale dataset management.
Build a minimal AnnData object with X, obs, and var, then save to h5ad.
High-intent search queries and answers about installing and using this skill.
AnnData is a data structure that stores biological measurements (X matrix), cell annotations (obs), gene metadata (var), and multi-dimensional data in a single object, then saves to h5ad format for efficient single-cell analysis workflows.
Yes. AnnData supports backed mode for memory-efficient operations on large h5ad files, sparse matrices, and lazy loading, enabling scalable analysis of multi-omics data without exhausting RAM.
AnnData handles h5ad, zarr, CSV, MTX, Loom, and 10X formats, allowing flexible I/O across common single-cell and multi-omics data sources.
AnnData provides subsetting, concatenation, and merging operations to combine datasets or extract cell and gene subsets while preserving annotations and multi-dimensional layers.
Yes. AnnData is the core container for Scanpy, Muon, and scverse tools, enabling seamless integration with single-cell analysis pipelines and deep learning frameworks.
bigbioConvert UCSC Cell Browser TSV matrices and metadata into AnnData objects.
jaechang-hitsAnalyze single-cell RNA-seq data with Scanpy from QC to marker identification.
LogauaEngstromCreate and manipulate annotated single-cell omics data matrices in Python.
ya-wayConvert single-cell data objects between Seurat and Scanpy formats.
