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、潜在嵌入、批次校正、差异表达及细胞注释。确保数据预处理、训练日志和结果的 reproducibility，并验证生物学一致性。

skills/scvi-tools/SKILL.md Companion-Inc/feynman

Trigger Scenarios

需要进行单细胞 RNA 测序数据分析请求 scVI 或 scANVI 模型训练与参数调优需要执行批次校正或差异表达分析要求生成可复现的 AnnData 分析结果

Install

npx skills add Companion-Inc/feynman --skill scvi-tools -g -y

More Options

Use without installing

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.