Agent Skills › companion-inc/feynman › scvi-tools

scvi-tools

GitHub

用于执行 scvi-tools 单细胞分析工作流，涵盖模型设置、潜空间嵌入、批次校正、差异表达及细胞注释等任务。强调可重复性，规范数据预处理、环境验证、结果保存及质量检查流程，确保原始与衍生数据分离。

skills/scvi-tools/SKILL.md companion-inc/feynman

触发场景

scVI/scANVI 模型设置单细胞数据批次校正差异表达分析细胞类型注释 AnnData 可重复分析

安装

npx skills add companion-inc/feynman --skill scvi-tools -g -y

更多选项

不安装直接使用

npx skills use companion-inc/feynman@scvi-tools

指定 Agent (Claude Code)

npx skills add companion-inc/feynman --skill scvi-tools -a claude-code -g -y

安装 repo 全部 skill

npx skills add companion-inc/feynman --all -g -y

预览 repo 内 skill

npx skills add companion-inc/feynman --list

SKILL.md

Frontmatter

{
    "name": "scvi-tools",
    "description": "Run scvi-tools single-cell workflows. Use when a task asks for scVI\/scANVI setup, latent embeddings, batch correction, differential expression, cell annotation, or reproducible AnnData analysis."
}

scvi-tools

Use this skill for reproducible scvi-tools analysis.

Workflow:

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

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