scvi-tools-single-cell

scvi-tools-single-cell is a skill for Claude Code from jaechang-hits/SciAgent-Skills. It costs 90 tokens per session (7,535 once invoked), scanned A, original, no licence file.

A Python workflow for analysing single-cell omics data, such as measurements from individual cells. It includes models for correcting batch differences, labelling cell types, combining RNA and protein data, and estimating differential expression with uncertainty.

In plain words
What is it for?
Use it with AnnData to train models and extract corrected data, annotations, transferred knowledge, and differential-expression results.
Why use it?
It helps researchers compare datasets made in different batches, assign cell labels, and account for uncertainty in biological results.

Skill for Claude Code

Written for Claude Code: shipped in a Claude Code plugin.

Part of the sciagent-skills plugin — 206 skills shipped together

Good fit Use it with AnnData to train models and extract corrected data, annotations, transferred knowledge, and differential-expression results.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/jaechang-hits/sciagent-skills/scvi-tools-single-cell
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 jaechang-hits/SciAgent-Skills --skill scvi-tools-single-cell
Clone the repo
git clone --depth 1 https://github.com/jaechang-hits/SciAgent-Skills

Made for: Claude Code.

Or install sciagent-skills, the plugin that ships this one along with the rest of its 206 skills.

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-single-cell

README.md
[![agentmods](https://agentmods.dev/badge/skills/jaechang-hits/sciagent-skills/scvi-tools-single-cell/github.svg)](https://agentmods.dev/skills/jaechang-hits/sciagent-skills/scvi-tools-single-cell)
Your own site
<a href="https://agentmods.dev/skills/jaechang-hits/sciagent-skills/scvi-tools-single-cell"><img src="https://agentmods.dev/badge/skills/jaechang-hits/sciagent-skills/scvi-tools-single-cell/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-single-cell

Your own site · 80×15
<a href="https://agentmods.dev/skills/jaechang-hits/sciagent-skills/scvi-tools-single-cell"><img src="https://agentmods.dev/badge/skills/jaechang-hits/sciagent-skills/scvi-tools-single-cell.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 90 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 7,535 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.
Origin unknown 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 $0.00090 $0.07535
Opus 5.5 $0.00036 $0.03014
Sonnet 5.5 $0.00018 $0.01507
Haiku 4.5 $0.00009 $0.00754

Measured 28d ago against content hash 1bf034a91723, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

scvi-tools-single-cell 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 28d 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/genomics-bioinformatics/single-cell/scvi-tools-single-cell/SKILL.md · 660 lines

The source is not reproduced here

A licence we could not identify

The repository carries a LICENSE file, but it is custom or dual enough that GitHub cannot name it and neither can this catalogue. Unknown terms are not permission, so the body is not copied here. Read the licence at the source and decide for yourself.

Read it on GitHub

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. 28d ago Changed · +69 lines 1bf034a91723
  2. 1mo ago First seen · 591 lines · 90 tokens per session scan A 2bad1629a9dd

Subscribe to this mod's changes

scvi-tools-single-cell is a skill published in the GitHub repository jaechang-hits/SciAgent-Skills (384 stars, last pushed 6d ago), with no licence file. It adds 90 tokens to every session and 7,535 once invoked, about $0.0004 per session on Opus 5.5. 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 2026-09-03.

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