celltypist-cell-annotation SKILL.md skillA
celltypist-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/celltypist-cell-annotation@git:20260929.7a7d60fPins git:20260929.7a7d60f 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/celltypist-cell-annotation/SKILL.md- Versions recorded
- 4
- Latest version
- git:20260929.7a7d60f, committed Sep 29, 2026
- First version recorded
- May 28, 2026
- Size
- 21,466 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Automated scRNA-seq cell type annotation via pre-trained logistic regression. 45+ models: immune, gut, lung, brain, fetal, cancer microenvironments. Input normalized AnnData; outputs per-cell labels, majority-vote cluster labels, confidence scores. Use for fast, reference-backed annotation without manual marker inspection.
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
# CellTypist Cell Type Annotation ## Overview CellTypist is an automated cell type classifier for single-cell RNA-seq data built on logistic regression models trained on curated reference atlases. Given a normalized AnnData object, it predicts cell type labels at the single-cell level and optionally applies majority voting within user-defined clusters to produce consensus, biologically coherent annotations. The tool ships with 45+ ready-to-use models spanning pan-immune, organ-specific, and developmental contexts, and supports training custom models from labeled data. ## When to Use - Annotating PBMC, whole-blood, lymph node, or other immune cell datasets using a single standardized reference model - Generating a first-pass cell type annotation before manual curation with canonical marker genes - Annotating cluster-level cell types in published or in-house datasets using majority voting to smooth noisy per-cell predictions - Comparing annotation results across multiple tissue-specific models to determine the most biologically relevant reference - Training a custom CellTypist model from a labeled reference dataset for a tissue or species not covered by pre-built models …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/celltypist-cell-annotation@sha256:2a822e5e021018eaThe line at the top of this page pins the label git:20260929.7a7d60f, 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_r5hvmt2wkb444zrc)
2 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 4 versions of this file, between May 28, 2026 and Sep 29, 2026, about one every 41 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260929.7a7d60f latest | 2026-09-29 | 7a7d60f | 21,466 B | A | view · diff |
| git:20260929.35fe6e3 | 2026-09-29 | 35fe6e3 | 21,515 B | A | view · diff |
| git:20260827.cbbeb75 | 2026-08-27 | cbbeb75 | 18,190 B | A | view · diff |
| git:20260528.3e3f998 | 2026-05-28 | 3e3f998 | 18,074 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 (21466 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_r5hvmt2wkb444zrc GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/celltypist-cell-annotation GET https://markdownregistry.com/api/v1/blob/2a822e5e021018eaf18b5af137a0e536da69a1a9b4ec27d8aa89cfa313f0bb04
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.