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scvi-tools
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  • 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
    • Multi-resolution deconvolution of spatial transcriptomics
    • Multi-resolution deconvolution of spatial transcriptomics in R
    • Introduction to gimVI
    • 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
    • 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.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.model.utils.mde
      • scvi._settings.ScviConfig
    • Developer
      • scvi.data.AnnDataManager
      • scvi.data.fields.BaseAnnDataField
      • scvi.data.fields.LayerField
      • scvi.data.fields.CategoricalObsField
      • scvi.data.fields.NumericalJointObsField
      • scvi.data.fields.CategoricalJointObsField
      • scvi.data.fields.ObsmField
      • scvi.data.fields.ProteinObsmField
      • 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.MuDataCategoricalObsField
      • scvi.data.fields.MuDataObsmField
      • scvi.data.fields.MuDataNumericalJointObsField
      • scvi.data.fields.MuDataCategoricalJointObsField
      • 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.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.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.external.gimvi.JVAE
      • scvi.external.cellassign.CellAssignModule
      • scvi.external.stereoscope.RNADeconv
      • scvi.external.stereoscope.SpatialDeconv
      • scvi.module.base.BaseModuleClass
      • scvi.module.base.PyroBaseModuleClass
      • scvi.module.base.LossRecorder
      • scvi.module.base.auto_move_data
      • scvi.nn.FCLayers
      • scvi.nn.Encoder
      • scvi.nn.Decoder
      • scvi.nn.one_hot
      • scvi.train.AdversarialTrainingPlan
      • scvi.train.PyroTrainingPlan
      • scvi.train.SemiSupervisedTrainingPlan
      • scvi.train.Trainer
      • scvi.train.TrainingPlan
      • scvi.train.TrainRunner
      • scvi.train.SaveBestState
      • scvi.train.LoudEarlyStopping
      • scvi.utils.track
      • scvi.utils.setup_anndata_dsp
      • scvi.utils.attrdict
    • Datasets
      • 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
    • New in 0.17.4 (2021-09-20)
    • New in 0.17.3 (2022-08-26)
    • New in 0.17.2 (2022-08-26)
    • New in 0.17.1 (2022-07-14)
    • New in 0.17.0 (2022-07-14)
    • New in 0.16.4 (2022-06-14)
    • New in 0.16.3 (2022-06-04)
    • New in 0.16.2 (2022-05-10)
    • New in 0.16.1 (2022-04-22)
    • New in 0.16.0 (2022-04-12)
    • New in 0.15.5 (2022-04-06)
    • New in 0.15.4 (2022-03-28)
    • New in 0.15.3 (2022-03-24)
    • New in 0.15.2 (2022-03-15)
    • New in 0.15.1 (2022-03-11)
    • New in 0.15.0 (2022-02-28)
    • New in 0.14.6 (2021-02-05)
    • New in 0.14.5 (2021-11-22)
    • New in 0.14.4 (2021-11-16)
    • New in 0.14.3 (2021-10-19)
    • New in 0.14.2 (2021-10-18)
    • New in 0.14.1 (2021-10-11)
    • New in 0.14.0 (2021-10-07)
    • New in 0.13.0 (2021-08-23)
    • New in 0.12.2 (2021-08-11)
    • New in 0.12.1 (2021-07-29)
    • New in 0.12.0 (2021-07-15)
    • New in 0.11.0 (2021-05-23)
    • New in 0.10.1 (2021-05-04)
    • New in 0.10.0 (2021-04-20)
    • New in 0.9.1 (2021-03-20)
    • New in 0.9.0 (2021-03-03)
    • New in 0.8.1 (2020-12-23)
    • New in 0.8.0 (2020-12-17)
    • New in 0.7.1 (2020-10-20)
    • New in 0.7.0 (2020-10-14)
    • scvi History
  • References
  • Contributing
  • Discussion
  • GitHub
  v: stable
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New in 0.12.2 (2021-08-11)#

Changes#

  • Updated OrderedDict typing import to support all Python 3.7 versions (#1114).

Breaking changes#

None!

Contributors#

  • @adamgayoso

  • @galenxing

  • @jjhong922

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  • New in 0.12.2 (2021-08-11)
    • Changes
    • Breaking changes
    • Contributors