scvi-tools
Train official scvi-tools models (scVI/scANVI/totalVI/PeakVI/MultiVI/veloVI) on raw counts after the scRNA gold chain. Use for probabilistic batch integration or those named models. Does not run DestVI/Cell2location. Do not log-normalize before setup_anndata.
Pinned to revision 683018420a75, so it is the text this page describes rather than whatever the author pushed since.
Files
- skills/scvi-tools/SKILL.md
- skills/scvi-tools/LICENSE.txt
- skills/scvi-tools/references/atac_peakvi.md
- skills/scvi-tools/references/batch_correction_sysvi.md
- skills/scvi-tools/references/citeseq_totalvi.md
- skills/scvi-tools/references/data_preparation.md
- skills/scvi-tools/references/environment_setup.md
- skills/scvi-tools/references/label_transfer.md
- skills/scvi-tools/references/multiome_multivi.md
- skills/scvi-tools/references/rna_velocity_velovi.md
- skills/scvi-tools/references/scarches_mapping.md
- skills/scvi-tools/references/scrna_integration.md
- skills/scvi-tools/references/spatial_deconvolution.md
- skills/scvi-tools/references/troubleshooting.md
- skills/scvi-tools/scripts/cluster_embed.py
- skills/scvi-tools/scripts/differential_expression.py
- skills/scvi-tools/scripts/hyperparam_search.py
- skills/scvi-tools/scripts/integrate_datasets.py
- skills/scvi-tools/scripts/model_utils.py
- skills/scvi-tools/scripts/prepare_data.py
- skills/scvi-tools/scripts/scvi_smoke.py
- skills/scvi-tools/scripts/train_model.py
- skills/scvi-tools/scripts/transfer_labels.py
- skills/scvi-tools/scripts/validate_adata.py
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