Contents Menu Expand Light mode Dark mode Auto light/dark mode
scvi-tools
Logo
  • Installation
  • Tutorials
    • Introduction to scvi-tools
    • Data loading and preparation
    • Using Python in R with reticulate
    • 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
    • PeakVI: Analyzing scATACseq data
    • ATAC-seq analysis in R
    • ScBasset: Analyzing scATACseq data
    • scBasset: Batch correction of scATACseq data
    • Multi-resolution deconvolution of spatial transcriptomics
    • Multi-resolution deconvolution of spatial transcriptomics in R
    • Introduction to gimVI
    • Spatial mapping with Tangram
    • 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
    • Using scvi-hub to download pretrained scvi-tools models
    • Using scvi-hub to upload pretrained scvi-tools models
    • Minification
    • Model hyperparameter tuning with scVI
    • Using autotune with a new model class
    • Stereoscope applied to left ventricule data
    • Mapping human lymph node cell types to 10X Visium with Cell2location
    • 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.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.autotune.ModelTuner
      • scvi.autotune.TuneAnalysis
      • scvi.hub.HubMetadata
      • scvi.hub.HubModelCardHelper
      • scvi.hub.HubModel
      • 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.dataloaders.AnnDataLoader
      • scvi.dataloaders.AnnTorchDataset
      • 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.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.LoudEarlyStopping
      • scvi.autotune.TunerManager
      • scvi.autotune.Tunable
      • scvi.autotune.TunableMixin
      • 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.seqfishplus
      • scvi.data.seqfish
      • scvi.data.smfish
      • 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
  v: stable
Versions
latest
stable
0.20.3
0.20.2
0.20.1
0.20.0
0.19.0
0.18.0
0.17.4
0.17.3
0.17.2
0.17.1
0.17.0
0.16.4
0.16.3
0.16.2
0.16.1
0.16.0
0.15.5
0.15.4
0.15.3
0.15.2
0.15.1
0.15.0
0.14.6
0.14.5
0.14.4
0.14.3
0.14.2
0.14.1
0.14.0
0.13.0
0.12.2
0.12.1
0.12.0
0.11.0
0.10.1
0.10.0
0.9.1
0.9.0
0.8.1
0.8.0
0.7.1
0.7.0
0.6.8
0.6.7
0.6.6
0.6.5
0.6.4
0.6.3
0.5.0_a
Downloads
On Read the Docs
Project Home
Builds
Back to top
Edit this page

scvi.data.fields.MuDataWrapper#

scvi.data.fields.MuDataWrapper(adata_field_cls, preregister_fn=None)[source]#

Wraps an AnnDataField with BaseMuDataWrapperClass.

Parameters:
  • adata_field_cls (Type[BaseAnnDataField]) – AnnDataField class to wrap.

  • preregister_fn (Optional[Callable]) – Function that will be called at the beginning of register_field() and transfer_field().

Return type:

Type[BaseAnnDataField]

Next
scvi.data.fields.MuDataLayerField
Previous
scvi.data.fields.BaseMuDataWrapperClass
Copyright © 2022, Yosef Lab, UC Berkeley
Made with Furo
On this page
  • scvi.data.fields.MuDataWrapper
    • MuDataWrapper()