h5mu-structure SKILL.md skillA
h5mu-structure from engreitzlab/perturbnmf is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add engreitzlab/perturbnmf/h5mu-structure@git:20260929.add0212Pins git:20260929.add0212 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- engreitzlab/perturbnmf
- Path
.claude/skills/h5mu-structure/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260929.add0212, committed Sep 29, 2026
- First version recorded
- May 13, 2026
- Size
- 4,186 bytes
- Repository stars
- 10
- License
- MIT
Inspect an .h5mu (MuData) file and generate a structured txt summary of its contents in a tree format. Lists all modalities, their X matrices, obs/var columns, uns, obsm, layers, obsp, varm, varp, and MuData-level attributes. Use this skill whenever the user asks to inspect, describe, summarize, or explore the structure of a .h5mu file, or when they want to know what's inside a MuData object saved on disk. Also trigger when the user says things like "what's in this h5mu…
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
# h5mu Structure Inspector When the user wants to inspect or summarize the structure of an `.h5mu` file, run the bundled Python script to generate a detailed tree-format summary. ## How to use 1. Identify the `.h5mu` file path the user wants to inspect. 2. Run the inspection script: ```bash python3 SKILL_DIR/scripts/inspect_h5mu.py <path_to_file.h5mu> ``` Replace `SKILL_DIR` with the actual path to this skill's directory (where this SKILL.md lives). 3. The script writes `<filename>_structure.txt` in the same directory as the input file and also prints the output to stdout. 4. Share the key findings with the user — modalities found, shapes, notable obs/var columns, what's stored in uns/obsm, etc. ## What the output contains For each modality in the MuData: - **X**: matrix type (sparse/dense), shape, dtype - **obs/**: all column names, with example obs_names (cell barcodes); each column annotated with its dtype, **how many unique items it contains**, and the **first 3 unique values** - **var/**: all column names, with example var_names (gene IDs); each column annotated with its dtype, **how many unique items it contains**, and the **first 3 unique values** …
Read the whole file at its exact version.
How to install
mdr add engreitzlab/perturbnmf/h5mu-structure@sha256:dc272532d3214e78The line at the top of this page pins the label git:20260929.add0212, 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_ptarfv6gtviq5dhw)
2 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 3 versions of this file, between May 13, 2026 and Sep 29, 2026, about one every 69 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260929.add0212 latest | 2026-09-29 | add0212 | 4,186 B | A | view · diff |
| git:20260806.31a4992 | 2026-08-06 | 31a4992 | 4,182 B | A | view · diff |
| git:20260513.0e22e2b | 2026-05-13 | 0e22e2b | 3,902 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (4186 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
engreitzlab/perturbnmf · 10 stars · license MIT · pushed 2026-10-20 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_ptarfv6gtviq5dhw GET https://markdownregistry.com/api/v1/resolve?ref=engreitzlab/perturbnmf/h5mu-structure GET https://markdownregistry.com/api/v1/blob/dc272532d3214e7895bf4b119b5f5a7a258aa4c257445f6e1d94b7eb42a2988e
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.