Analyze single-cell data with scvi-tools, using deep learning to combine datasets, correct differences between experiments, and transfer cell labels. Model guides and reusable scripts cover RNA, protein, chromatin accessibility, spatial data, and downstream analysis.
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Deep learning for single-cell analysis using scvi-tools. This skill should be used when users need (1) data integration and batch correction with scVI/scANVI, (2) ATAC-seq analysis with PeakVI, (3) CITE-seq multi-modal analysis with totalVI, (4) multiome RNA+ATAC analysis with MultiVI, (5) spatial transcriptomics deconvolution with DestVI, (6) label transfer and reference mapping with scANVI/scArches, (7) RNA velocity with veloVI, or (8) any deep learning-based single-cell method. Triggers include mentions of scVI, scANVI, totalVI, PeakVI, MultiVI, DestVI, veloVI, sysVI, scArches, variational autoencoder, VAE, batch correction, data integration, multi-modal, CITE-seq, multiome, reference mapping, latent space.
安装前可以查看交给 AI 代理的指令内容。
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)
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Review a design or web page against WCAG 2.1 AA, an accessibility standard. Organize findings on contrast, keyboard access, forms, and screen reader behavior, with severity levels and practical recommendations for fixes.
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Build a single brief on an existing customer using available sales records, emails, documents, call notes, and internal chat. Understand the current situation, key contacts, recent discussions, and gaps that may need attention.
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Build or refresh a strategic customer account plan from sales records, emails, and meeting transcripts. Organize goals, stakeholders, growth opportunities, risks, and dated actions into a document, then sync approved highlights to the customer relationship management system.
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Research prospective companies and contacts, check existing customer records, and assess fit against your ideal customer profile. Receive a sourced brief covering recent developments, likely priorities, outreach talking points, and a suggested next step.
中文简介正在准备中。当前显示英语简介。
Research sales accounts using Common Room data to summarize company details, buying signals, ownership, and key contacts. Answer specific questions directly or prepare a broader briefing with evidence-based next steps, clearly identifying missing information.
中文简介正在准备中。当前显示英语简介。
Score and group accounts by customer fit and engagement, such as recent contact and open sales opportunities. Identify where to focus sales effort, choose next actions, and spot promising accounts with neglected outreach or missing information.
中文简介正在准备中。当前显示英语简介。