Create, read, and write AnnData objects with backed storage for large single-cell datasets.
npx skills add https://github.com/rubensliv/k-dense-ai --skill anndata-rubensliv
Please help me install this Agent Skill. Skill: anndata Source: https://github.com/rubensliv/k-dense-ai/tree/main/scientific-skills/anndata Command: npx skills add https://github.com/rubensliv/k-dense-ai --skill anndata-rubensliv
AnnData provides a scalable, structured container for annotated data matrices used in single-cell genomics, enabling efficient storage, retrieval, and manipulation of X, obs, var, and multi-dimensional annotations.
Create an AnnData object from a small matrix with basic obs/var metadata and run a quick quality control check.
High-intent search queries and answers about installing and using this skill.
AnnData provides backed storage for large single-cell data matrices, enabling memory-efficient reading, writing, and manipulation of datasets without loading them entirely into memory.
You can subset, filter, and concatenate scRNA-seq data while preserving multi-dimensional annotations like obs, var, and embeddings, ensuring metadata stays intact during transformations.
AnnData objects integrate seamlessly with Scanpy and the scverse ecosystem, supporting end-to-end workflows from data preparation and QC to normalization and reproducible pipeline building.
An AnnData object structures single-cell genomics data using core components: X for the data matrix, obs and var for annotations, layers for alternative representations, and uns for unstructured metadata.
The best way to prepare scRNA-seq data is creating an AnnData object to structure the matrix and metadata, then applying quality control and normalization steps integrated directly within Scanpy workflows.
Backed storage supports diverse I/O formats for large datasets, allowing efficient reading and writing of annotated data matrices while maintaining compatibility with the broader PyData ecosystem.
ilove323Integrate and analyze single-cell genomics data with scvi-tools pipelines.
tondevrelAnalyze single-cell gene expression data with AnnData and scRNA-seq workflows.
crazymsnManage annotated single-cell matrices with AnnData objects for scalable analysis.
K-Dense-AICreate, read, write, and manipulate AnnData objects for single-cell analyses.
