anndata-data-structure SKILL.md skillA
anndata-data-structure from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/anndata-data-structure@git:20260528.3e3f998Pins git:20260528.3e3f998 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/genomics-bioinformatics/single-cell/anndata-data-structure/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260528.3e3f998, committed May 28, 2026
- Size
- 23,287 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Annotated matrices for single-cell genomics. Stores X with obs/var metadata, layers, embeddings (obsm/varm), graphs (obsp/varp), uns. Use for .h5ad/.zarr I/O, concatenation, scverse integration. For analysis use scanpy; for probabilistic models use scvi-tools.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# AnnData — Annotated Data Matrices for Single-Cell Genomics ## Overview AnnData provides the standard data structure for single-cell genomics in the scverse ecosystem. It stores an observations-by-variables matrix (X) alongside cell metadata (obs), gene metadata (var), layers, embeddings (obsm/varm), graphs (obsp/varp), and unstructured metadata (uns). Supports sparse matrices, H5AD/Zarr storage, backed mode for large files, and integration with Scanpy, scvi-tools, and Muon. ## When to Use - Constructing annotated matrices from raw count data with cell/gene metadata - Reading/writing `.h5ad` or `.zarr` files for single-cell experiments - Subsetting cells by quality metrics, gene sets, or metadata conditions - Concatenating multiple experimental batches with consistent metadata - Storing multiple data layers (raw counts, normalized, scaled) in one object - Working with large datasets exceeding RAM (backed mode, lazy concatenation) - Preparing data for Scanpy or scvi-tools pipelines - For single-cell **analysis** (clustering, DE, visualization), use `scanpy` instead - For **probabilistic models**, use `scvi-tools` instead ## Prerequisites …
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How to install
mdr add jaechang-hits/sciagent-skills/anndata-data-structure@sha256:3c3a60572c0dbf0fThe line at the top of this page pins the label git:20260528.3e3f998, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_xp6wg72u24gxzyf6)
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Versions
The registry has recorded 1 version of this file, committed on May 28, 2026.
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Source
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
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