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
    • 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.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 0.15.4 (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: 0.15.4
Versions
latest
stable
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

New in 0.15.4 (2022-03-28)#

Changes#

  • Add peakVI publication reference #1463.

  • Update notebooks with new install functionality for Colab #1466.

  • Simplify changing the training plan for pyro #1470.

  • Optionally scale ELBO by a scalar in PyroTrainingPlan #1469.

Bug fixes#

Contributors#

  • @jjhong922

  • @adamgayoso

  • @vitkl

Next
New in 0.15.3 (2022-03-24)
Previous
Release notes
Copyright © 2021, Yosef Lab, UC Berkeley
Made with Furo
Contents
  • New in 0.15.4 (2022-03-28)
    • Changes
    • Bug fixes
    • Contributors