Skip to main content
Ctrl+K
scvi-tools - Home
  • Scverse
  • GitHub
  • Discourse
  • Model hub
  • 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
    • 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
    • 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
      • 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
      • Using scvi-hub to download pretrained scvi-tools models
      • Using scvi-hub to upload pretrained scvi-tools models
      • Minification
    • Hyperparameter tuning
      • Model hyperparameter tuning with scVI
      • Using autotune with a new model class
    • Development
      • Data handling in scvi-tools
      • Constructing a probabilistic module
      • Constructing a high-level model
  • 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.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.ModelTuner
      • scvi.autotune.TuneAnalysis
      • scvi.hub.HubMetadata
      • scvi.hub.HubModelCardHelper
      • scvi.hub.HubModel
      • scvi.criticism.PosteriorPredictiveCheck
      • scvi.model.utils.mde
      • 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.NegativeBinomial
      • scvi.distributions.NegativeBinomialMixture
      • scvi.distributions.ZeroInflatedNegativeBinomial
      • scvi.distributions.JaxNegativeBinomialMeanDisp
      • 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.PyroSviTrainMixin
      • scvi.model.base.PyroSampleMixin
      • scvi.model.base.PyroJitGuideWarmup
      • scvi.model.base.PyroModelGuideWarmup
      • scvi.model.base.DifferentialComputation
      • 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.module.base.BaseModuleClass
      • scvi.module.base.BaseMinifiedModeModuleClass
      • scvi.module.base.PyroBaseModuleClass
      • scvi.module.base.JaxBaseModuleClass
      • scvi.module.base.LossOutput
      • scvi.module.base.auto_move_data
      • scvi.nn.FCLayers
      • scvi.nn.Encoder
      • scvi.nn.Decoder
      • scvi.nn.one_hot
      • 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.SaveCheckpoint
      • scvi.train.LoudEarlyStopping
      • scvi.autotune.TunerManager
      • scvi.utils.track
      • scvi.utils.setup_anndata_dsp
      • scvi.utils.attrdict
    • 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
  • Release notes
  • References
  • Contributing
  • Discussion
  • GitHub
  • Model hub
  • .md

Multimodal

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

previous

PoissonVI: Analyzing quantitative scATAC-seq fragment counts

next

CITE-seq analysis with totalVI

By The scvi-tools development team

© Copyright 2023, The scvi-tools development team..