bio-machine-learning-atlas-mapping SKILL.md skillA
bio-machine-learning-atlas-mapping from fridrichmethod/awesome-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add fridrichmethod/awesome-skills/bio-machine-learning-atlas-mapping@git:20260628.aa12f9bPins git:20260628.aa12f9b in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- fridrichmethod/awesome-skills
- Path
skills/atlas-mapping/SKILL.md- Versions recorded
- 4
- Latest version
- git:20260628.aa12f9b, committed Jun 28, 2026
- First version recorded
- May 17, 2026
- Size
- 20,616 bytes
- Repository stars
- 15
- License
- a license file GitHub does not identify
Maps query single-cell data onto reference atlases and transfers cell-type labels using scArches surgery (scVI/scANVI), Symphony, Azimuth, CellTypist, scPoli, popV, and foundation models, with explicit out-of-distribution and label-transfer uncertainty. Use when annotating new single-cell datasets against a pre-trained reference, deciding which mapping method fits, or judging whether transferred labels are trustworthy. For de novo clustering and manual annotation see…
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
## Version Compatibility
Reference examples tested with: anndata 0.10+, scanpy 1.10+, scvi-tools 1.1+, scikit-learn 1.3+, celltypist 1.6+.
Before using code patterns, verify installed versions match. If versions differ:
- Python: `pip show <package>` then `help(module.function)` to check signatures
scvi-tools 1.x has had API churn around minified/registered models and the semi-supervised loader. Confirm `scvi.__version__` and `help(scvi.model.SCANVI.load_query_data)` before relying on argument names. If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
# Reference Mapping and Label Transfer for Single-Cell Data
**"Annotate my scRNA-seq query against a reference atlas"** -> Project query cells into a fixed reference latent space and transfer labels, then gate every label on an out-of-distribution signal.
- scArches surgery: `scvi.model.SCANVI.prepare_query_anndata()` -> `load_query_data()` -> `train(plan_kwargs={'weight_decay': 0.0})` -> `predict(soft=True)`
- Linear/fixed reference: Symphony (R) or Azimuth/Seurat anchor transfer
…Read the whole file at its exact version.
How to install
mdr add fridrichmethod/awesome-skills/bio-machine-learning-atlas-mapping@sha256:2f0ca4b735b8d4c2The line at the top of this page pins the label git:20260628.aa12f9b, 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_23mvjpckgkovl24y)
1 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 4 versions of this file, between May 17, 2026 and Jun 28, 2026, about one every 14 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260628.aa12f9b latest | 2026-06-28 | aa12f9b | 20,616 B | A | view · diff |
| git:20260607.d890519 | 2026-06-07 | d890519 | 20,619 B | A | view · diff |
| git:20260531.6e617c4 | 2026-05-31 | 6e617c4 | 5,915 B | A | view · diff |
| git:20260517.81511a7 | 2026-05-17 | 81511a7 | 5,918 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 (20616 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
fridrichmethod/awesome-skills · 15 stars · license a license file GitHub does not identify · pushed 2026-10-18 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_23mvjpckgkovl24y GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bio-machine-learning-atlas-mapping GET https://markdownregistry.com/api/v1/blob/2f0ca4b735b8d4c23236cbae0c08b12b11ff1b70eb54523166905148647f0dfe
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.