single-cell-annotation SKILL.md skillA
single-cell-annotation 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/single-cell-annotation@git:20260528.7303680Pins git:20260528.7303680 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
legacy/single-cell-annotation/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260528.7303680, committed May 28, 2026
- Size
- 12,811 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches.
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
# Single Cell RNA-seq Cell Type Annotation --- ## Metadata **Short Description**: Best practices for annotating cell types in single-cell RNA-seq data using marker-based, automated, and reference-based approaches. **Authors**: Distilled from "Single-cell best practices" by Luecken, M.D. et al. **Affiliations**: Helmholtz Munich, Wellcome Sanger Institute, Harvard Medical School, and contributors **Version**: 1.0 **Last Updated**: January 2025 **License**: CC BY 4.0 **Commercial Use**: ✅ Allowed **Source**: https://www.sc-best-practices.org/cellular_structure/annotation.html **Citation**: Luecken, M.D., Theis, F.J. et al. (2023). Current best practices in single-cell RNA-seq analysis: a tutorial. Molecular Systems Biology. --- ## Overview Cell type annotation is the process of assigning cell type labels to clusters or individual cells in single-cell RNA-seq data. This guide covers three main approaches and their practical implementation. ## Key Concepts ### Cell Type vs. Cell State …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/single-cell-annotation@sha256:9ef521fca1a8dbe0The line at the top of this page pins the label git:20260528.7303680, 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_4r36akwlkg6xlhnp)
4 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on May 28, 2026.
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 (12811 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
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_4r36akwlkg6xlhnp GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/single-cell-annotation GET https://markdownregistry.com/api/v1/blob/9ef521fca1a8dbe01f980b1f0e8b14930c52dc3b2d789772e927c5d04338aa7e
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.