Guidance for scvi-tools, a Python toolkit that uses deep-learning models to analyze biological single-cell data. It covers methods for combining datasets, correcting batch differences, and working with RNA, ATAC, protein, and spatial data.

Use it for scVI or scANVI integration, PeakVI ATAC-seq analysis, totalVI CITE-seq analysis, MultiVI RNA-plus-ATAC analysis, and spatial transcriptomics.

It helps researchers choose and use scvi-tools methods when single-cell datasets come from different batches or measure several biological signals.

scvi-tools — Skill for Claude Code and Codex by giadaf-boosha

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 giadaf-boosha/claude-code --skill bio-research-scvi-tools

Clone the repo

git clone --depth 1 https://github.com/giadaf-boosha/claude-code

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.

README.md

[![agentmods](https://agentmods.dev/badge/skills/giadaf-boosha/claude-code/bio-research-scvi-tools/github.svg)](https://agentmods.dev/skills/giadaf-boosha/claude-code/bio-research-scvi-tools)

Your own site

<a href="https://agentmods.dev/skills/giadaf-boosha/claude-code/bio-research-scvi-tools"><img src="https://agentmods.dev/badge/skills/giadaf-boosha/claude-code/bio-research-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.

Your own site · 80×15

<a href="https://agentmods.dev/skills/giadaf-boosha/claude-code/bio-research-scvi-tools"><img src="https://agentmods.dev/badge/skills/giadaf-boosha/claude-code/bio-research-scvi-tools.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 193 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 1,867 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.

Model	Per session	Once invoked
Fable 5.1	$0.00193	$0.01867
Opus 5	$0.00097	$0.00933
Sonnet 5	$0.00039	$0.00373
Haiku 4.5	$0.00019	$0.00187

Measured 10d ago against content hash 03a69b32b77d, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-10, 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.

The scan reads SKILL.md. This mod also ships 8 executable files (scripts/cluster_embed.py, scripts/differential_expression.py, scripts/integrate_datasets.py, …), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

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/bio-research-scvi-tools/SKILL.md · 156 lines

The source is not reproduced here

No licence file

Read it on GitHub

Files

What ships with it

21 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

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.

10d ago First seen · 156 lines · 193 tokens per session scan A 03a69b32b77d

Subscribe to this mod's changes

scvi-tools is a skill published in the GitHub repository giadaf-boosha/claude-code (11 stars, last pushed yesterday), with no licence file. It adds 193 tokens to every session and 1,867 once invoked, about $0.0010 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 2026-08-31.

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