Load, save, subset, concatenate, and restructure AnnData objects across h5ad and zarr formats.
npx skills add https://github.com/jasrajtulsi/GRAD-SCOPE --skill anndata-jasrajtulsi
Please help me install this Agent Skill. Skill: anndata Source: https://github.com/jasrajtulsi/GRAD-SCOPE/tree/main/.claude/skills/anndata Command: npx skills add https://github.com/jasrajtulsi/GRAD-SCOPE --skill anndata-jasrajtulsi
This Skill removes the friction of working with annotated matrices in single-cell and other high-dimensional analysis workflows. It helps you read, write, structure, subset, and combine AnnData objects while keeping observations, variables, layers, embeddings, and metadata aligned.
Use the anndata skill to help me load a .h5ad file, inspect its metadata, and suggest the safest way to subset and save it for downstream single-cell analysis.
High-intent search queries and answers about installing and using this skill.
To load and inspect a single-cell h5ad file, read the AnnData object into memory and access its X matrix alongside obs and var metadata. This ensures observations and variables remain aligned for immediate scverse or Scanpy workflows.
Concatenating multiple single-cell batches involves merging AnnData objects while preserving observations, variables, and layers. You can combine batches and maintain metadata integrity across obs and var to ensure seamless downstream analysis.
Yes, backed mode and sparse matrices enable memory-efficient AnnData processing for large datasets. These best-practice workflows allow chunked processing and categorical handling without loading entire high-dimensional matrices into memory.
AnnData supports saving and loading zarr formats alongside h5ad, csv, mtx, and loom for robust data exchange. This I/O interoperability allows you to structure and save annotated matrices for scverse-compatible preparation.
Subsetting and filtering cells or genes preserves AnnData metadata alignment by automatically adjusting obs, var, layers, and embeddings simultaneously. This restructuring maintains metadata integrity during transformations without manual index correction.
robotlearning123Manage and analyze AnnData objects for single-cell genomics research.
StarlitnightlyCompare Leiden, Louvain, GMM, and scICE clustering backends on AnnData embeddings.
jackspaceManage annotated data matrices with AnnData for single-cell genomics analysis.
tony-zhelonkinConvert multi-assay Seurat objects to Python AnnData/MuData containers.
