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Installation
Tutorials
Quick start
Introduction to scvi-tools
Data loading and preparation
Using Python in R with
reticulate
scRNA-seq
Atlas-level integration of lung data
Integrating datasets with scVI in R
Integration and label transfer with Tabula Muris
Reference mapping with scvi-tools
Querying the Human Lung Cell Atlas
Seed labeling with scANVI
Linearly decoded VAE
Identification of zero-inflated genes
Annotation with CellAssign
Topic Modeling with Amortized LDA
Differential expression on C. elegans data
Isolating perturbation-induced variations with contrastiveVI
Benchmarking the scANVI fix
MrVI Quick Start Tutorial
Integration of scRNA-seq data with substantial batch effects using sysVI
Decipher Quick Start Tutorial
Variational inference for RNA velocity with VeloVI
ATAC-seq
PeakVI: Analyzing scATACseq data
ATAC-seq analysis in R
ScBasset: Analyzing scATACseq data
scBasset: Batch correction of scATACseq data
PoissonVI: Analyzing quantitative scATAC-seq fragment counts
scBS-seq
Integrating single-cell methylation data from different scBS-seq experiments with methylVI
Multimodal
CITE-seq analysis with totalVI
Integration of CITE-seq and scRNA-seq data
CITE-seq reference mapping with totalVI
CITE-seq analysis in R
Joint analysis of paired and unpaired multiomic data with MultiVI
Spatial transcriptomics
ResolVI to address noise and biases in spatial transcriptomics
Multi-resolution deconvolution of spatial transcriptomics
Multi-resolution deconvolution of spatial transcriptomics in R
Introduction to gimVI
Spatial mapping with Tangram
Stereoscope applied to left ventricule data
Mapping human lymph node cell types to 10X Visium with Cell2location
Model hub
Use pretrained models of scVI-hub for CELLxGENE
Using scvi-hub to download pretrained scvi-tools models
Using scvi-hub to upload pretrained scvi-tools models
Common Modelling Use Cases
Model hyperparameter tuning with scVI
Minification
Using SHAP values and IntegratedGradients for cell type classification interpretability
Development
Data handling in scvi-tools
Constructing a probabilistic module
Constructing a high-level model
Frequently asked questions
User guide
API
User
scvi.model.AUTOZI
scvi.model.CondSCVI
scvi.model.DestVI
scvi.model.LinearSCVI
scvi.model.PEAKVI
scvi.model.SCANVI
scvi.model.SCVI
scvi.model.TOTALVI
scvi.model.MULTIVI
scvi.model.AmortizedLDA
scvi.model.JaxSCVI
scvi.external.CellAssign
scvi.external.GIMVI
scvi.external.RNAStereoscope
scvi.external.SpatialStereoscope
scvi.external.SOLO
scvi.external.SCAR
scvi.external.Tangram
scvi.external.SCBASSET
scvi.external.ContrastiveVI
scvi.external.POISSONVI
scvi.external.VELOVI
scvi.external.MRVI
scvi.external.METHYLVI
scvi.external.METHYLANVI
scvi.external.Decipher
scvi.external.RESOLVI
scvi.external.SysVI
scvi.data.read_h5ad
scvi.data.read_csv
scvi.data.read_loom
scvi.data.read_text
scvi.data.read_10x_atac
scvi.data.read_10x_multiome
scvi.data.poisson_gene_selection
scvi.data.organize_cite_seq_10x
scvi.data.organize_multiome_anndatas
scvi.data.add_dna_sequence
scvi.data.reads_to_fragments
scvi.autotune.run_autotune
scvi.autotune.AutotuneExperiment
scvi.hub.HubMetadata
scvi.hub.HubModelCardHelper
scvi.hub.HubModel
scvi.criticism.PosteriorPredictiveCheck
scvi.model.utils.get_minified_adata_scrna
scvi._settings.ScviConfig
Developer
scvi.data.AnnDataManager
scvi.data.AnnDataManagerValidationCheck
scvi.data.fields.BaseAnnDataField
scvi.data.fields.LayerField
scvi.data.fields.CategoricalObsField
scvi.data.fields.CategoricalVarField
scvi.data.fields.NumericalJointObsField
scvi.data.fields.NumericalJointVarField
scvi.data.fields.CategoricalJointObsField
scvi.data.fields.CategoricalJointVarField
scvi.data.fields.ObsmField
scvi.data.fields.VarmField
scvi.data.fields.ProteinObsmField
scvi.data.fields.StringUnsField
scvi.data.fields.LabelsWithUnlabeledObsField
scvi.data.fields.BaseMuDataWrapperClass
scvi.data.fields.MuDataWrapper
scvi.data.fields.MuDataLayerField
scvi.data.fields.MuDataProteinLayerField
scvi.data.fields.MuDataNumericalObsField
scvi.data.fields.MuDataNumericalVarField
scvi.data.fields.MuDataCategoricalObsField
scvi.data.fields.MuDataCategoricalVarField
scvi.data.fields.MuDataObsmField
scvi.data.fields.MuDataVarmField
scvi.data.fields.MuDataNumericalJointObsField
scvi.data.fields.MuDataNumericalJointVarField
scvi.data.fields.MuDataCategoricalJointObsField
scvi.data.fields.MuDataCategoricalJointVarField
scvi.data.AnnTorchDataset
scvi.dataloaders.AnnDataLoader
scvi.dataloaders.ConcatDataLoader
scvi.dataloaders.DataSplitter
scvi.dataloaders.SemiSupervisedDataLoader
scvi.dataloaders.SemiSupervisedDataSplitter
scvi.distributions.Poisson
scvi.distributions.NegativeBinomial
scvi.distributions.NegativeBinomialMixture
scvi.distributions.ZeroInflatedNegativeBinomial
scvi.distributions.JaxNegativeBinomialMeanDisp
scvi.distributions.BetaBinomial
scvi.model.base.BaseModelClass
scvi.model.base.BaseMinifiedModeModelClass
scvi.model.base.VAEMixin
scvi.model.base.RNASeqMixin
scvi.model.base.ArchesMixin
scvi.model.base.UnsupervisedTrainingMixin
scvi.model.base.SemisupervisedTrainingMixin
scvi.model.base.PyroSviTrainMixin
scvi.model.base.PyroSampleMixin
scvi.model.base.PyroJitGuideWarmup
scvi.model.base.PyroModelGuideWarmup
scvi.model.base.DifferentialComputation
scvi.model.base.EmbeddingMixin
scvi.module.AutoZIVAE
scvi.module.Classifier
scvi.module.LDVAE
scvi.module.MRDeconv
scvi.module.PEAKVAE
scvi.module.MULTIVAE
scvi.module.SCANVAE
scvi.module.TOTALVAE
scvi.module.VAE
scvi.module.VAEC
scvi.module.AmortizedLDAPyroModule
scvi.module.JaxVAE
scvi.external.gimvi.JVAE
scvi.external.cellassign.CellAssignModule
scvi.external.stereoscope.RNADeconv
scvi.external.stereoscope.SpatialDeconv
scvi.external.tangram.TangramMapper
scvi.external.scbasset.ScBassetModule
scvi.external.contrastivevi.ContrastiveVAE
scvi.external.velovi.VELOVAE
scvi.external.mrvi.MRVAE
scvi.external.methylvi.METHYLVAE
scvi.external.methylvi.METHYLANVAE
scvi.external.decipher.DecipherPyroModule
scvi.external.resolvi.RESOLVAE
scvi.external.sysvi.SysVAE
scvi.module.base.BaseModuleClass
scvi.module.base.BaseMinifiedModeModuleClass
scvi.module.base.SupervisedModuleClass
scvi.module.base.PyroBaseModuleClass
scvi.module.base.JaxBaseModuleClass
scvi.module.base.EmbeddingModuleMixin
scvi.module.base.LossOutput
scvi.module.base.auto_move_data
scvi.nn.FCLayers
scvi.nn.Encoder
scvi.nn.Decoder
scvi.nn.DecoderSCVI
scvi.nn.one_hot
scvi.nn.Embedding
scvi.train.AdversarialTrainingPlan
scvi.train.SemiSupervisedTrainingPlan
scvi.train.LowLevelPyroTrainingPlan
scvi.train.PyroTrainingPlan
scvi.train.JaxTrainingPlan
scvi.train.Trainer
scvi.train.TrainingPlan
scvi.train.TrainRunner
scvi.train.SaveBestState
scvi.train.ScibCallback
scvi.train.SaveCheckpoint
scvi.train.LoudEarlyStopping
scvi.utils.track
scvi.utils.setup_anndata_dsp
scvi.utils.attrdict
scvi.model.get_max_epochs_heuristic
scvi.external.decipher.utils.Trajectory
Datasets
scvi.data.cellxgene
scvi.data.pbmc_seurat_v4_cite_seq
scvi.data.spleen_lymph_cite_seq
scvi.data.heart_cell_atlas_subsampled
scvi.data.pbmcs_10x_cite_seq
scvi.data.purified_pbmc_dataset
scvi.data.dataset_10x
scvi.data.brainlarge_dataset
scvi.data.pbmc_dataset
scvi.data.cortex
scvi.data.smfish
scvi.data.synthetic_iid
scvi.data.breast_cancer_dataset
scvi.data.mouse_ob_dataset
scvi.data.retina
scvi.data.prefrontalcortex_starmap
scvi.data.frontalcortex_dropseq
Developer documentation
Contributing code
Maintenance guide
Release notes
References
Discussion
GitHub
Model hub
.md
.pdf
scBS-seq
scBS-seq
#
Integrating single-cell methylation data from different scBS-seq experiments with methylVI
