k-dense-ai/scientific-agent-skills · skills/scanpy/SKILL.md

scanpy skillA

scanpy is agent-read markdown (skill) from k-dense-ai/scientific-agent-skills: Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, visualization, and converting R-friendly single-cell formats such as Seurat or SingleCellExperiment RDS files into h5ad for Scanpy. Best for exploratory scRNA-seq analysis with established workflows. For deep learning models use scvi-tools; for data format questions use anndata..

Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns the same grade.

How to install

Latest version
mdr add k-dense-ai/scientific-agent-skills/scanpy@v1.6
Exact content
mdr add k-dense-ai/scientific-agent-skills/scanpy@sha256:aad13ea7d74dc80c

Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.

Badge

mdr badge

[![mdr](https://markdownregistry.com/badge/art_cjo5wck5dz4s2rg4.svg)](https://markdownregistry.com/a/art_cjo5wck5dz4s2rg4)

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Versions

versioncommittedcommitsizeaudit
v1.6 latest2026-09-02 1e5eeff 16,586 BA view · diff
v1.52026-07-28 4fb7e0b 15,628 BA view · diff
v1.42026-07-26 2f2022d 15,628 BA view · diff
v1.32026-07-26 b085e11 20,727 BA view · diff
git:20260612.cb5a7c82026-06-12 cb5a7c8 20,732 BA view

Audit of the latest version

A  17 of 17 checks passed. Deterministic, no model, same answer every run.
  • pass: Frontmatter block present
  • pass: Frontmatter declares a name
  • pass: Frontmatter declares a description
  • pass: Size between 200 bytes and 200 KB (16586 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

GitHub

k-dense-ai/scientific-agent-skills · 45,352 stars · license MIT · pushed 2026-09-14 · 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/aad13ea7d74dc80c99b31fdd3d7f937b27f67d91d413941e8c28bb6c2504754c

Agents talk at modelranch.com: hand yours the instructions there and it joins the network that reads files like this one.