anndata
Handles annotated matrices in single-cell analysis, .h5ad and Zarr files
by k-dense-aiFree
Description
anndata is an agent skill for working with AnnData, a Python package for annotated data matrices. An AnnData object stores measurements in a main matrix, with metadata for observations and variables and multi-dimensional annotations alongside. It began in single-cell genomics through Scanpy and is now a general framework for any annotated data that needs efficient storage and analysis. The skill covers creating, reading and writing AnnData objects, working with h5ad and Zarr files, and performing single-cell RNA-seq analysis. It also covers large datasets with sparse matrices or backed mode, concatenating datasets or experimental batches, subsetting and filtering, and integrating with scanpy, scvi-tools and other tools in the scverse ecosystem. Use it when a task involves those data structures or formats. The skill is part of the k-dense-ai scientific agent skills repository on GitHub, which has about 49,600 stars. The listing shows it as free, and it has about 1,800 installs. Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk. Install it with npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill anndata.…
Highlights
- Creates, reads and writes AnnData objects
- Works with h5ad and Zarr files
- Single-cell RNA-seq analysis
- Sparse matrices and backed mode for large data
- Integrates with scanpy and the scverse ecosystem
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anndata FAQ
What is AnnData?
A Python package for annotated data matrices, storing measurements alongside observation and variable metadata.
Where did it come from?
It was designed for single-cell genomics through Scanpy, and it is now a general framework for annotated data.
What file formats does it use?
h5ad and Zarr, among other genomics data formats.
Does it handle large datasets?
The skill covers sparse matrices and backed mode for large datasets.
How do I install it?
Run npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill anndata.
Is it checked for security?
Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.
What are the best anndata alternatives?
Popular alternatives to anndata include arboreto, scanpy and scvelo. See all anndata alternatives