菜单
Deep learning for single-cell analysis using scvi-tools: data integration, batch correction, multi-modal analysis, reference mapping, and more.
默认使用会先检查来源的 Prompt；你也可以切换为直接命令，或下载本地副本。
决定是否安装前，请先阅读 SKILL.md，以及 SkillsMP 当前展示的配套文件。
用 Codex 或 Claude 帮你安装 复制这段 Prompt，粘贴到 Codex、Claude 或其他助手里，让它检查 Skill 页面并帮你完成安装。
直接命令不会经过审查 Prompt；运行前请先检查来源。
npx skills add https://github.com/vamseeachanta/workspace-hub --skill scvi-tools命令会保持在同一行。复制前请横向滚动并检查完整内容。
想先保存到本地？可下载 SkillsMP 当前能够提供的文件。
基于 SOC 职业分类
正在显示 SKILL.md
| name | scvi-tools |
| description | Deep learning for single-cell analysis using scvi-tools: data integration, batch correction, multi-modal analysis, reference mapping, and more. |
| type | reference |
| version | 1.0.0 |
| category | science |
| last_updated | "2026-02-03T00:00:00.000Z" |
| source | https://github.com/anthropics/knowledge-work-plugins |
| related_skills | ["single-cell-rna-qc","nextflow-pipelines","clinical-trial-protocol","instrument-data-allotrope","scientific-problem-selection"] |
| capabilities | [] |
| requires | [] |
| see_also | [] |
| tags | [] |
| scripts_exempt | true |
This skill provides guidance for deep learning-based single-cell analysis using scvi-tools, the leading framework for probabilistic models in single-cell genomics.
scripts/ to avoid rewriting common codereferences/environment_setup.mdreferences/troubleshooting.md| Data Type | Model | Primary Use Case |
|---|---|---|
| scRNA-seq | scVI | Unsupervised integration, DE, imputation |
| scRNA-seq + labels | scANVI | Label transfer, semi-supervised integration |
| CITE-seq (RNA+protein) | totalVI | Multi-modal integration, protein denoising |
| scATAC-seq | PeakVI | Chromatin accessibility analysis |
| Multiome (RNA+ATAC) | MultiVI | Joint modality analysis |
| Spatial + scRNA reference | DestVI | Cell type deconvolution |
| RNA velocity | veloVI | Transcriptional dynamics |
| Cross-technology | sysVI | System-level batch correction |
| Workflow | Reference File | Description |
|---|---|---|
| Environment Setup |
references/environment_setup.md |
| Installation, GPU, version info |
| Data Preparation | references/data_preparation.md | Formatting data for any model |
| scRNA Integration | references/scrna_integration.md | scVI/scANVI batch correction |
| ATAC-seq Analysis | references/atac_peakvi.md | PeakVI for accessibility |
| CITE-seq Analysis | references/citeseq_totalvi.md | totalVI for protein+RNA |
| Multiome Analysis | references/multiome_multivi.md | MultiVI for RNA+ATAC |
| Spatial Deconvolution | references/spatial_deconvolution.md | DestVI spatial analysis |
| Label Transfer | references/label_transfer.md | scANVI reference mapping |
| scArches Mapping | references/scarches_mapping.md | Query-to-reference mapping |
| Batch Correction | references/batch_correction_sysvi.md | Advanced batch methods |
| RNA Velocity | references/rna_velocity_velovi.md | veloVI dynamics |
| Troubleshooting | references/troubleshooting.md | Common issues and solutions |
Modular scripts for common workflows. Chain together or modify as needed.
| Script | Purpose | Usage |
|---|---|---|
prepare_data.py | QC, filter, HVG selection | python scripts/prepare_data.py raw.h5ad prepared.h5ad --batch-key batch |
train_model.py | Train any scvi-tools model | python scripts/train_model.py prepared.h5ad results/ --model scvi |
cluster_embed.py | Neighbors, UMAP, Leiden | python scripts/cluster_embed.py adata.h5ad results/ |
differential_expression.py | DE analysis | python scripts/differential_expression.py model/ adata.h5ad de.csv --groupby leiden |
transfer_labels.py | Label transfer with scANVI | python scripts/transfer_labels.py ref_model/ query.h5ad results/ |
integrate_datasets.py | Multi-dataset integration | python scripts/integrate_datasets.py results/ data1.h5ad data2.h5ad |
validate_adata.py | Check data compatibility | python scripts/validate_adata.py data.h5ad --batch-key batch |
# 1. Validate input data
python scripts/validate_adata.py raw.h5ad --batch-key batch --suggest
# 2. Prepare data (QC, HVG selection)
python scripts/prepare_data.py raw.h5ad prepared.h5ad --batch-key batch --n-hvgs 2000
# 3. Train model
python scripts/train_model.py prepared.h5ad results/ --model scvi --batch-key batch
# 4. Cluster and visualize
python scripts/cluster_embed.py results/adata_trained.h5ad results/ --resolution 0.8
# 5. Differential expression
python scripts/differential_expression.py results/model results/adata_clustered.h5ad results/de.csv --groupby leiden
The scripts/model_utils.py provides importable functions for custom workflows:
| Function | Purpose |
|---|---|
prepare_adata() | Data preparation (QC, HVG, layer setup) |
train_scvi() | Train scVI or scANVI |
evaluate_integration() | Compute integration metrics |
get_marker_genes() | Extract DE markers |
save_results() | Save model, data, plots |
auto_select_model() | Suggest best model |
quick_clustering() | Neighbors + UMAP + Leiden |
Raw counts required: scvi-tools models require integer count data
adata.layers["counts"] = adata.X.copy() # Before normalization
scvi.model.SCVI.setup_anndata(adata, layer="counts")
HVG selection: Use 2000-4000 highly variable genes
sc.pp.highly_variable_genes(adata, n_top_genes=2000, batch_key="batch", layer="counts", flavor="seurat_v3")
adata = adata[:, adata.var['highly_variable']].copy()
Batch information: Specify batch_key for integration
scvi.model.SCVI.setup_anndata(adata, layer="counts", batch_key="batch")
Need to integrate scRNA-seq data?
├── Have cell type labels? → scANVI (references/label_transfer.md)
└── No labels? → scVI (references/scrna_integration.md)
Have multi-modal data?
├── CITE-seq (RNA + protein)? → totalVI (references/citeseq_totalvi.md)
├── Multiome (RNA + ATAC)? → MultiVI (references/multiome_multivi.md)
└── scATAC-seq only? → PeakVI (references/atac_peakvi.md)
Have spatial data?
└── Need cell type deconvolution? → DestVI (references/spatial_deconvolution.md)
Have pre-trained reference model?
└── Map query to reference? → scArches (references/scarches_mapping.md)
Need RNA velocity?
└── veloVI (references/rna_velocity_velovi.md)
Strong cross-technology batch effects?
└── sysVI (references/batch_correction_sysvi.md)