scvi-tools

scvi-tools is a skill for Claude Code, Codex from companion-inc/feynman. It costs 44 tokens per session (185 once invoked), scanned A, original, MIT.

A workflow for analysing single-cell biology data with scvi-tools, a Python toolkit for studying individual cells and their gene activity. It works with AnnData, a common file format for annotated biological datasets.

In plain words
What is it for?
Use it for cell-data embeddings, batch correction, gene-expression comparisons, cell-type annotation, and analysis of AnnData files.
Why use it?
It helps keep data preparation, model settings, training results, and checks in one reproducible record while accounting for differences between batches.

Skill for Claude CodeCodex

Written for no agent in particular: nothing here depends on one.

Good fit Use it for cell-data embeddings, batch correction, gene-expression comparisons, cell-type annotation, and analysis of AnnData files.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/companion-inc/feynman/scvi-tools
About the project

Feynman is an open-source AI research agent that helps users investigate topics with language models. It supports local model providers and hosted model authentication through its setup process. The catalogue contains skills, agents, and instructions that extend Feynman’s workflows.

companion-inc/feynman · 8,870 stars · on GitHub · feynman.is

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add companion-inc/feynman --skill scvi-tools
Clone the repo
git clone --depth 1 https://github.com/companion-inc/feynman

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for scvi-tools

README.md
[![agentmods](https://agentmods.dev/badge/skills/companion-inc/feynman/scvi-tools/github.svg)](https://agentmods.dev/skills/companion-inc/feynman/scvi-tools)
Your own site
<a href="https://agentmods.dev/skills/companion-inc/feynman/scvi-tools"><img src="https://agentmods.dev/badge/skills/companion-inc/feynman/scvi-tools/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for scvi-tools

Your own site · 80×15
<a href="https://agentmods.dev/skills/companion-inc/feynman/scvi-tools"><img src="https://agentmods.dev/badge/skills/companion-inc/feynman/scvi-tools.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 44 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 185 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe. Third-party audits
  • NVIDIA SkillSpector pass 7 Sept 2026
How audits are shown
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00044 $0.00185
Opus 5 $0.00022 $0.00093
Sonnet 5 $0.00009 $0.00037
Haiku 4.5 $0.00004 $0.00018

Measured 10d ago against content hash eb31f53f93f7, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-09, from the pricing page.

Security

Grade A, and why

scvi-tools scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 10d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

skills/scvi-tools/SKILL.md · 19 lines

What it actually says

scvi-tools

Use this skill for reproducible scvi-tools analysis.

Workflow:

  1. Record AnnData path, organism, assay, batch keys, label keys, covariates, train/test split, and filtering choices.
  2. Verify Python environment, GPU/CPU route, package version, and data availability before training.
  3. Save preprocessing notebook, model parameters, training logs, latent embeddings, differential-expression tables, and plots.
  4. Check batch mixing, biological separation, marker consistency, and sensitivity to preprocessing choices.
  5. Attach exact commands and artifact paths to the final summary.

Keep raw counts, normalized values, and model-derived latent variables clearly separated.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 10d ago First seen · 19 lines · 44 tokens per session scan A eb31f53f93f7

Subscribe to this mod's changes

scvi-tools is a skill published in the GitHub repository companion-inc/feynman (8,870 stars, last pushed 14d ago), licensed MIT. It adds 44 tokens to every session and 185 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

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