scanpy SKILL.md skillA
scanpy from k-dense-ai/scientific-agent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add k-dense-ai/scientific-agent-skills/scanpy@v1.8Pins v1.8 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- k-dense-ai/scientific-agent-skills
- Path
skills/scanpy/SKILL.md- Versions recorded
- 7
- Latest version
- v1.8, committed Oct 1, 2026
- First version recorded
- Jun 12, 2026
- Size
- 20,277 bytes
- Repository stars
- 56,497
- License
- MIT
Performs Scanpy single-cell RNA-seq QC, normalization, HVG selection, PCA/UMAP/t-SNE, clustering, exploratory marker ranking, pseudobulk preparation, visualization, and Seurat or SingleCellExperiment RDS conversion to h5ad. Applies to established exploratory scRNA-seq workflows with explicit count and expression provenance; complementary skills cover scvi-tools models and AnnData format details.
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 Analysis ## Overview Scanpy is a scalable Python toolkit for analyzing single-cell RNA-seq data, built on AnnData. Apply this skill for complete single-cell workflows including quality control, normalization, dimensionality reduction, clustering, marker gene identification, visualization, and trajectory analysis. Targets **Scanpy 1.12.4** (released 2026-08-27), reviewed 2026-10-01. Native synthetic tests establish data/API contracts, not biological validity. ## Installation Requires Python **3.12+** (scanpy 1.12 dropped Python ≤3.11) and anndata **≥0.10**. ```bash uv pip install "scanpy[leiden]" ``` The `[leiden]` extra installs `igraph` and `leidenalg`; the scripts explicitly select `flavor="igraph"`. For reproducible environments, pin a version: `uv pip install "scanpy[leiden]==1.12.4"`. For large or out-of-core datasets, many functions support [Dask](https://docs.dask.org/) arrays (experimental): ```bash uv pip install "scanpy[leiden]" dask ``` …
Read the whole file at its exact version.
How to install
mdr add k-dense-ai/scientific-agent-skills/scanpy@sha256:4a59f87933a1e9edThe line at the top of this page pins the label v1.8, 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_cjo5wck5dz4s2rg4)
4 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 7 versions of this file, between Jun 12, 2026 and Oct 1, 2026, about one every 19 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| v1.8 latest | 2026-10-01 | a92663a | 20,277 B | A | view · diff |
| v1.7 | 2026-09-30 | ce9e6e9 | 16,917 B | A | view · diff |
| v1.6 | 2026-09-02 | 1e5eeff | 16,586 B | A | view · diff |
| v1.5 | 2026-07-28 | 4fb7e0b | 15,628 B | A | view · diff |
| v1.4 | 2026-07-26 | 2f2022d | 15,628 B | A | view · diff |
| v1.3 | 2026-07-26 | b085e11 | 20,727 B | A | view · diff |
| git:20260612.cb5a7c8 | 2026-06-12 | cb5a7c8 | 20,732 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 (20277 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
k-dense-ai/scientific-agent-skills · 56,497 stars · license MIT · pushed 2026-11-02 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_cjo5wck5dz4s2rg4 GET https://markdownregistry.com/api/v1/resolve?ref=k-dense-ai/scientific-agent-skills/scanpy GET https://markdownregistry.com/api/v1/blob/4a59f87933a1e9ed49eac603719af1b0c606dd99050fe59ffa1c1bf807900cb8
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.
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