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AnnData Single-Cell Data Format

Lets the agent create, read, write, subset and combine annotated data matrices (.h5ad, Zarr) using AnnData 0.13

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
6 files

What it does

Once installed, the agent knows how to work with AnnData, a Python format for storing a table of measurements (such as gene activity per cell) together with labels describing its rows and columns. It can build these objects, read and write common file types like .h5ad and Zarr, filter and subset them, and concatenate several datasets while following the current 0.13 API rules. It is a data-format helper; analysis workflows are pointed to other skills such as scanpy.

Great for

  • Bioinformatics or single-cell researchers who need correct AnnData code
  • Developers building pipelines that read or write .h5ad or Zarr files
  • Students learning how annotated matrices are structured

Skip it if

  • Full analysis workflows like clustering or cell-type annotation, which the skill itself says belong to scanpy (wrong tool, lower quality output)
  • Users who need guaranteed results on sensitive or clinical data without checking the code, since the examples are illustrative and not validated on real datasets

Try asking

  • “Create an AnnData object from my count matrix with cell and gene metadata and save it as an h5ad file”
  • “Concatenate these three batch files along observations and keep track of which batch each cell came from”
  • “Open a large h5ad file in backed read mode and extract a subset without loading everything into memory”
  • “Convert my Zarr store to CSV and explain what information might be lost”
Step-by-step guide: how to use AnnData Single-Cell Data FormatInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 6 original files, the MIT licence and an attribution note.

    anndata.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip anndata.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip anndata.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Pin the anndata version as the skill recommends, since APIs changed in 0.13 (for example ad.concat replaces AnnData.concatenate)
  • Close backed file handles and check outputs when writing lossy formats such as CSV, which may densify the matrix
  • Ask for scanpy or scvi-tools when your task goes beyond data structure and I/O

What's inside

  • references/best_practices.md
  • references/concatenation.md
  • references/data_structure.md
  • references/io_operations.md
  • references/manipulation.md
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.