Skills

scgpt

scgpt is a skill in aipoch/open-science, last changed 7 Sept 2026. It can reach the network and name web addresses. Our pattern check flagged nothing at commit a77f531 on 27 Oct 2026.

Pattern check: nothing flagged · commit a77f531 · 27 Oct 2026

Install
From the author
Embed and annotate single-cell expression data with scGPT, a foundation model for single-cell biology. Use this skill when: (1) Producing cell embeddings from an AnnData for clustering/integration, (2) Zero-shot or fine-tuned cell-type annotation, (3) Gene-level representation for perturbation/GRN tasks. For probabilistic single-cell models (scVI etc.), use the scvi-tools library.
Licence
Apache 2.0
Repo stars
5.4k
Folder last changed
7 Sept 2026 (opens in a new tab)
Publisher
aipoch
Files
2 files
Checked
a77f531 (opens in a new tab) · 27 Oct 2026

Install

Each tab says whether it installs commit a77f531, the one we checked, or the latest version.

No tab for your agent? Use Any agent for OpenCode, Goose, Windsurf (Devin Desktop), Zed, Roo Code, Factory Droid, Junie, Amp and Antigravity, and Claude Code for Cline. Kiro needs the folder copied by hand.

Pinned to commit a77f531, the one we checked.

From your project's root folder:

tmp="$(mktemp -d)" &&
  git clone -q --depth 1 --filter=blob:none --no-checkout https://github.com/aipoch/open-science.git "$tmp" &&
  git -C "$tmp" fetch -q --depth 1 origin a77f53199bb62c1b871af82446d38da6969d38e1 &&
  git -C "$tmp" sparse-checkout set -- resources/skills/scgpt &&
  git -C "$tmp" checkout -q a77f53199bb62c1b871af82446d38da6969d38e1 &&
  mkdir -p .claude/skills &&
  mkdir .claude/skills/scgpt &&
  cp -R "$tmp"/resources/skills/scgpt/. .claude/skills/scgpt/ &&
  rm -rf "$tmp"

If Claude Code was already running and this created the skills folder, run /reload-skills.

Claude Code docs (opens in a new tab)

What it can touch

From the files and frontmatter at commit a77f531. This is how much a skill can do, not whether it is risky.

What it can touch: Scripts or outside hosts

  • Reaches the network

    It sends or fetches data over the internet, for example with curl, an HTTP library or a package install.

  • Names web addresses

    It mentions outside web addresses the agent may visit. We list them but don't follow them.

Pattern check

Pattern check: nothing flagged · commit a77f531 · 27 Oct 2026

We checked every text file in this skill, at commit a77f531 on 27 Oct 2026, against 45 published patterns such as download-and-run commands, hidden text and credential access. We don't run the skill, we don't read the web pages it points to, and we can't judge everything its instructions might lead an agent to do. In published tests, pattern checks like this one missed most malicious skills. Read the skill before you install it — especially anything it asks you to download or run.

How the check worksReport an incorrect finding

Outside links we did not follow

  • https://github.com/bowang-lab/scGPT

Format check

Each agent reads SKILL.md a little differently. We check the file against each one's published rules; we don't run the skill in any agent.

  • Agent Skills specPasses with warnings

    The open format from agentskills.io, held to what the strictest agents enforce, so one folder loads everywhere.

    • Warning

      The frontmatter uses [ ] or { } values. Most agents accept them, but the spec's validator (skills-ref) rejects the file. F4

      Fix: Write lists as "- item" lines and maps as indented key: value lines, without anchors or tags.

    • Warning

      Fields outside the spec: category and requirements. Uploads to the Claude apps and API, and the spec's validator, reject the file; most agents ignore these fields. O1

      Fix: Delete them for a portable skill, or keep them if you only target the agents that read them.

    • Warning

      metadata values should be text; third_party (a list) is not. The spec's validator turns them into text; other readers may not. O4

      Fix: Quote each value, for example version: "1.0".

  • Claude CodePasses

    Claude Code reads its own extra fields, ignores unknown ones, and still loads a skill whose frontmatter is broken, without its fields.

    • Note

      Claude Code ignores fields it doesn't know: category and requirements. O1

      Fix: Check the spelling against Claude Code's field list, or delete them.

  • Claude apps & API uploadFails

    Uploading to claude.ai or the Claude API, or packaging with Anthropic's script, accepts only the six spec fields and stops on anything else.

    • Error

      Upload and packaging fail on fields outside the spec: category and requirements. O1

      Fix: Delete them, and keep your own data under metadata as text values.

    • Note

      The description is 383 characters. The claude.ai Help Center says 200 at most, though Anthropic's API docs and validator allow 1,024. D4

      Fix: If the claude.ai upload refuses it, trim the description to 200 characters.

    • Note

      metadata values should be text; third_party (a list) is not. The spec defines metadata as text to text. O4

      Fix: Quote each value, for example version: "1.0".

  • OpenAI (Codex & API)Passes with warnings

    Codex finds SKILL.md by its exact name and needs a description; OpenAI's Skills API checks the frontmatter against the spec and caps uploads.

    • Warning

      Fields outside the spec: category and requirements. Codex ignores them; OpenAI doesn't say whether its upload accepts them. O1

      Fix: Delete them, or move your own data under metadata as text values.

    • Warning

      metadata values should be text; third_party (a list) is not. OpenAI's upload follows the spec's text-to-text rule. O4

      Fix: Quote each value, for example version: "1.0".

  • VS Code & CopilotPasses

    VS Code reads skills one folder below .github/skills, .claude/skills or .agents/skills and falls back to the folder name when the name is missing or differs; GitHub's Copilot docs require the exact name SKILL.md.

    • Note

      VS Code ignores fields it doesn't support: category and requirements. O1

      Fix: Delete them unless another agent you target reads them.

SKILL.md

Files

2 files

PathSize
.catalog_stamp (opens in a new tab)13 B
SKILL.md (opens in a new tab)5.8 KB

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