scanpy-scrna-seq SKILL.md skillA
scanpy-scrna-seq 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/scanpy-scrna-seq@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/scanpy-scrna-seq/SKILL.md- Versions recorded
- 4
- Latest version
- git:20260929.7a7d60f, committed Sep 29, 2026
- First version recorded
- May 28, 2026
- Size
- 18,907 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
scRNA-seq with Scanpy: QC, normalization, HVG selection, PCA, neighborhood graph, UMAP/t-SNE, Leiden clustering, markers, cell annotation, trajectory inference. Standard scRNA-seq exploration.
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
# Scanpy Single-Cell RNA-seq Analysis ## Overview Scanpy is a scalable Python toolkit for analyzing single-cell RNA-seq data built on the AnnData format. This skill covers the end-to-end standard workflow: quality control, normalization, highly variable gene selection, dimensionality reduction, clustering, marker gene identification, and cell type annotation. It produces annotated datasets and publication-quality visualizations. ## When to Use - Analyzing single-cell RNA-seq count matrices (10X Genomics, h5ad, CSV, loom) - Performing quality control filtering on scRNA-seq datasets (mitochondrial %, gene counts) - Running dimensionality reduction: PCA, UMAP, t-SNE - Identifying cell clusters via Leiden community detection - Finding differentially expressed marker genes per cluster (Wilcoxon, t-test, logistic regression) - Annotating cell types from known marker gene panels - Conducting trajectory inference and pseudotime analysis (PAGA, diffusion pseudotime) - Generating publication-quality single-cell plots (dot plots, heatmaps, stacked violins) - Comparing gene expression across experimental conditions within cell types …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/scanpy-scrna-seq@sha256:ef8f32f42d48c6c5The 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_pofegkqnxiomnp72)
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 | 18,907 B | A | view · diff |
| git:20260929.35fe6e3 | 2026-09-29 | 35fe6e3 | 18,956 B | A | view · diff |
| git:20260827.cbbeb75 | 2026-08-27 | cbbeb75 | 15,921 B | A | view · diff |
| git:20260528.3e3f998 | 2026-05-28 | 3e3f998 | 15,780 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 (18907 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_pofegkqnxiomnp72 GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/scanpy-scrna-seq GET https://markdownregistry.com/api/v1/blob/ef8f32f42d48c6c5d39a92a7356ce0c37f106fe855a178ad006eebceed620fe7
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.