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Agent Skill

Scgpt skill

scgptaipoch/open-scienceresources/skills/scgpt/SKILL.md

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.

5.3kApache-2.0

always on

89 tokname + description

once used

1,097 tokSKILL.md body

bundled files

11 KB

repo stars

5.3kGitHub

Install the Scgpt skill

Skills CLI (Claude Code, Codex, Cursor and others)

npx skills add https://github.com/aipoch/open-science --skill scgpt

Claude Code, by hand (all projects)

git clone --depth 1 https://github.com/aipoch/open-science.git /tmp/open-science
mkdir -p ~/.claude/skills
cp -R /tmp/open-science/resources/skills/scgpt ~/.claude/skills/scgpt

For one project only, copy the folder into .claude/skills/ in that project instead. The agent picks it up when a task matches its description.

What it costs your context

Agent Skills load in three steps. Tokens counted with the o200k tokenizer; your model's count will differ a little.

WhenWhat loadsCost
Every sessionName and description89 tok
When the agent uses itThe SKILL.md instructions1,097 tok
Only if opened1 bundled files (1 KB)varies

Until it is used, scgpt costs about 15× less than the median MCP server we measured (1,362 tokens on every turn). Installing all 25 skills from aipoch/open-science would load 2,130 tokens of descriptions. Skills vs MCP study

Checks

Our checks found nothing to flag: it follows the Agent Skills specification's naming and size guidelines and doesn't pipe downloads into a shell.

Checked 2026-10-22 · method

What's inside

The headings of its SKILL.md. Read the full file on GitHub.

  • scGPT — Single-Cell Foundation Model
  • Prerequisites
  • How to run
  • Loading the vocabulary and checkpoint
  • Embedding an AnnData
  • Output format
  • Remote compute
  • Gotchas
  • Troubleshooting

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  3. borzoiaipoch/open-science

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  5. compute-env-setupaipoch/open-science

    Prepare reproducible setup instructions and validate a user-managed named software environment on an Open-Science SSH Compute Host, including direct SSH and Slurm hosts. Use when a remote job needs packages, modules, cache variables, or a repeatable activation that the host does not already provide.

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  6. customizeaipoch/open-science

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  7. diffdockaipoch/open-science

    Predict small-molecule binding poses with DiffDock-L (Corso et al. 2023/2024, github.com/gcorso/DiffDock) — blind diffusion docking that places a ligand into a protein pocket without a predefined search box and ranks the samples with a learned confidence model. Reach for this skill to dock a SMILES or SDF against a PDB, to generate ranked 3D poses for a small fragment library, or to get a starting pose for downstream rescoring. DiffDock predicts geometry, not affinity.

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