scVI
0.6.8
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Package Reference
scvi.dataset Package
scvi.inference Package
scvi.models Package
scvi.models.modules Module
scVI
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Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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X
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Z
A
accuracy() (scvi.inference.Posterior method)
AdapterTrainer (class in scvi.inference)
AlternateSemiSupervisedTrainer (class in scvi.inference)
AnnDatasetFromAnnData (class in scvi.dataset)
apply_t_sne() (scvi.inference.Posterior static method)
AutoZIVAE (class in scvi.models)
B
batch_indices (scvi.dataset.GeneExpressionDataset attribute)
BrainLargeDataset (class in scvi.dataset)
BrainSmallDataset (class in scvi.dataset)
BreastCancerDataset (class in scvi.dataset)
C
CbmcDataset (class in scvi.dataset)
cell_types_to_labels() (scvi.dataset.GeneExpressionDataset method)
CellMeasurement (class in scvi.dataset)
check_training_status() (scvi.inference.Trainer method)
CiteSeqDataset (class in scvi.dataset)
Classifier (class in scvi.models)
ClassifierTrainer (class in scvi.inference)
classify() (scvi.models.SCANVI method)
(scvi.models.VAEC method)
clustering_scores() (scvi.inference.Posterior method)
collate_fn_base() (scvi.dataset.GeneExpressionDataset method)
collate_fn_builder() (scvi.dataset.GeneExpressionDataset method)
compute_elbo() (scvi.inference.TotalPosterior method)
compute_global_kl_divergence() (scvi.models.AutoZIVAE method)
compute_library_size_batch() (scvi.dataset.GeneExpressionDataset method)
compute_marginal_log_likelihood() (scvi.inference.TotalPosterior method)
compute_metrics() (scvi.inference.Trainer method)
compute_predictions() (scvi.inference.ClassifierTrainer method)
compute_reconstruction_error() (scvi.inference.TotalPosterior method)
corrupt() (scvi.dataset.GeneExpressionDataset method)
corrupt_posteriors() (scvi.inference.Trainer method)
corrupted() (scvi.inference.Posterior method)
(scvi.inference.TotalPosterior method)
corrupted_X (scvi.dataset.GeneExpressionDataset attribute)
CortexDataset (class in scvi.dataset)
create_posterior() (scvi.inference.SemiSupervisedTrainer method)
(scvi.inference.Trainer method)
CsvDataset (class in scvi.dataset)
cuda() (scvi.models.AutoZIVAE method)
D
data_loaders_loop() (scvi.inference.JVAETrainer method)
(scvi.inference.Trainer method)
Dataset10X (class in scvi.dataset)
decode() (scvi.models.JVAE method)
Decoder (class in scvi.models.modules)
DecoderSCVI (class in scvi.models.modules)
DecoderTOTALVI (class in scvi.models.modules)
default_metrics_to_monitor (scvi.inference.JVAETrainer attribute)
(scvi.inference.TotalTrainer attribute)
(scvi.inference.Trainer attribute)
(scvi.inference.UnsupervisedTrainer attribute)
differential_expression_score() (scvi.inference.Posterior method)
(scvi.inference.TotalPosterior method)
differential_expression_stats() (scvi.inference.Posterior method)
(scvi.inference.TotalPosterior method)
download() (scvi.dataset.DownloadableDataset method)
DownloadableAnnDataset (class in scvi.dataset)
DownloadableDataset (class in scvi.dataset)
E
elbo() (scvi.inference.Posterior method)
(scvi.inference.TotalPosterior method)
encode() (scvi.models.JVAE method)
Encoder (class in scvi.models.modules)
EncoderTOTALVI (class in scvi.models.modules)
entropy_batch_mixing() (scvi.inference.Posterior method)
F
FCLayers (class in scvi.models.modules)
FILENAME (scvi.dataset.SyntheticRandomDataset attribute)
filter_cell_types() (scvi.dataset.GeneExpressionDataset method)
filter_cells_by_attribute() (scvi.dataset.GeneExpressionDataset method)
filter_cells_by_count() (scvi.dataset.GeneExpressionDataset method)
filter_genes_by_attribute() (scvi.dataset.GeneExpressionDataset method)
filter_genes_by_count() (scvi.dataset.GeneExpressionDataset method)
find_path_to_data() (scvi.dataset.Dataset10X method)
forward() (scvi.models.AutoZIVAE method)
(scvi.models.Classifier method)
(scvi.models.JVAE method)
(scvi.models.modules.Decoder method)
(scvi.models.modules.DecoderSCVI method)
(scvi.models.modules.DecoderTOTALVI method)
(scvi.models.modules.Encoder method)
(scvi.models.modules.EncoderTOTALVI method)
(scvi.models.modules.FCLayers method)
(scvi.models.modules.LinearDecoderSCVI method)
(scvi.models.modules.MultiDecoder method)
(scvi.models.modules.MultiEncoder method)
(scvi.models.SCANVI method)
(scvi.models.TOTALVI method)
(scvi.models.VAE method)
(scvi.models.VAEC method)
FrontalCortexDropseqDataset (class in scvi.dataset)
G
GeneExpressionDataset (class in scvi.dataset)
generate() (scvi.inference.Posterior method)
(scvi.inference.TotalPosterior method)
generate_denoised_samples() (scvi.inference.Posterior method)
(scvi.inference.TotalPosterior method)
generate_feature_correlation_matrix() (scvi.inference.Posterior method)
(scvi.inference.TotalPosterior method)
generate_parameters() (scvi.inference.Posterior method)
(scvi.inference.TotalPosterior method)
genes_to_index() (scvi.dataset.GeneExpressionDataset method)
get_alphas_betas() (scvi.models.AutoZIVAE method)
get_batch_mask_cell_measurement() (scvi.dataset.GeneExpressionDataset method)
get_bayes_factors() (scvi.inference.Posterior method)
get_discriminator_confusion() (scvi.inference.JVAETrainer method)
get_imputed_values() (scvi.inference.JVAETrainer method)
get_latent() (scvi.inference.JVAETrainer method)
(scvi.inference.Posterior method)
(scvi.inference.TotalPosterior method)
get_latents() (scvi.models.SCANVI method)
(scvi.models.VAE method)
get_loadings() (scvi.models.LDVAE method)
get_loss_magnitude() (scvi.inference.JVAETrainer method)
get_normalized_denoised_expression() (scvi.inference.TotalPosterior method)
get_protein_background_mean() (scvi.inference.TotalPosterior method)
get_protein_mean() (scvi.inference.TotalPosterior method)
get_reconstruction_loss() (scvi.models.AutoZIVAE method)
(scvi.models.TOTALVI method)
(scvi.models.VAE method)
get_sample_dispersion() (scvi.models.TOTALVI method)
get_sample_dropout() (scvi.inference.TotalPosterior method)
get_sample_mixing() (scvi.inference.TotalPosterior method)
get_sample_rate() (scvi.models.JVAE method)
(scvi.models.TOTALVI method)
(scvi.models.VAE method)
get_sample_scale() (scvi.inference.Posterior method)
(scvi.inference.TotalPosterior method)
(scvi.models.TOTALVI method)
(scvi.models.VAE method)
get_stats() (scvi.inference.Posterior method)
H
HematoDataset (class in scvi.dataset)
I
identity() (in module scvi.models.modules)
imputation() (scvi.inference.Posterior method)
(scvi.inference.TotalPosterior method)
imputation_benchmark() (scvi.inference.Posterior method)
imputation_list() (scvi.inference.Posterior method)
(scvi.inference.TotalPosterior method)
imputation_score() (scvi.inference.Posterior method)
indices (scvi.inference.Posterior attribute)
inference() (scvi.models.AutoZIVAE method)
(scvi.models.TOTALVI method)
(scvi.models.VAE method)
initialize_cell_attribute() (scvi.dataset.GeneExpressionDataset method)
initialize_cell_measurement() (scvi.dataset.GeneExpressionDataset method)
initialize_gene_attribute() (scvi.dataset.GeneExpressionDataset method)
initialize_mapped_attribute() (scvi.dataset.GeneExpressionDataset method)
J
JointSemiSupervisedTrainer (class in scvi.inference)
JVAE (class in scvi.models)
JVAETrainer (class in scvi.inference)
K
kl_weight (scvi.inference.UnsupervisedTrainer attribute)
knn_purity() (scvi.inference.Posterior method)
L
labels (scvi.dataset.GeneExpressionDataset attribute)
LDVAE (class in scvi.models)
LinearDecoderSCVI (class in scvi.models.modules)
load_posterior() (in module scvi.inference)
LoomDataset (class in scvi.dataset)
loss() (scvi.inference.AlternateSemiSupervisedTrainer method)
(scvi.inference.ClassifierTrainer method)
(scvi.inference.JVAETrainer method)
(scvi.inference.SemiSupervisedTrainer method)
(scvi.inference.TotalTrainer method)
(scvi.inference.UnsupervisedTrainer method)
loss_discriminator() (scvi.inference.JVAETrainer method)
(scvi.inference.TotalTrainer method)
M
make_gene_names_lower() (scvi.dataset.GeneExpressionDataset method)
map_cell_types() (scvi.dataset.GeneExpressionDataset method)
marginal_ll() (scvi.inference.Posterior method)
(scvi.inference.TotalPosterior method)
mask() (scvi.dataset.SyntheticDatasetCorr method)
(scvi.dataset.ZISyntheticDatasetCorr method)
merge_cell_types() (scvi.dataset.GeneExpressionDataset method)
module
scvi.dataset
scvi.inference
scvi.models
scvi.models.modules
MouseOBDataset (class in scvi.dataset)
MultiDecoder (class in scvi.models.modules)
MultiEncoder (class in scvi.models.modules)
N
nb_cells (scvi.dataset.GeneExpressionDataset attribute)
(scvi.inference.Posterior attribute)
nb_genes (scvi.dataset.GeneExpressionDataset attribute)
nn_overlap_score() (scvi.inference.Posterior method)
norm_X (scvi.dataset.GeneExpressionDataset attribute)
normalize() (scvi.dataset.GeneExpressionDataset method)
O
on_epoch_begin() (scvi.inference.JVAETrainer method)
(scvi.inference.Trainer method)
on_epoch_end() (scvi.inference.SemiSupervisedTrainer method)
(scvi.inference.Trainer method)
on_iteration_begin() (scvi.inference.Trainer method)
on_iteration_end() (scvi.inference.Trainer method)
on_training_begin() (scvi.inference.Trainer method)
(scvi.inference.UnsupervisedTrainer method)
on_training_end() (scvi.inference.Trainer method)
(scvi.inference.UnsupervisedTrainer method)
on_training_loop() (scvi.inference.JVAETrainer method)
(scvi.inference.TotalTrainer method)
(scvi.inference.Trainer method)
one_vs_all_degenes() (scvi.inference.Posterior method)
P
PbmcDataset (class in scvi.dataset)
populate() (scvi.dataset.BrainLargeDataset method)
(scvi.dataset.CiteSeqDataset method)
(scvi.dataset.CortexDataset method)
(scvi.dataset.CsvDataset method)
(scvi.dataset.Dataset10X method)
(scvi.dataset.DownloadableAnnDataset method)
(scvi.dataset.DownloadableDataset method)
(scvi.dataset.HematoDataset method)
(scvi.dataset.LoomDataset method)
(scvi.dataset.PbmcDataset method)
(scvi.dataset.PurifiedPBMCDataset method)
(scvi.dataset.SeqfishDataset method)
(scvi.dataset.SeqFishPlusDataset method)
(scvi.dataset.SmfishDataset method)
(scvi.dataset.SyntheticRandomDataset method)
populate_from_data() (scvi.dataset.GeneExpressionDataset method)
populate_from_datasets() (scvi.dataset.GeneExpressionDataset method)
populate_from_per_batch_list() (scvi.dataset.GeneExpressionDataset method)
populate_from_per_label_list() (scvi.dataset.GeneExpressionDataset method)
Posterior (class in scvi.inference)
posterior_type (scvi.inference.Posterior attribute)
posteriors_loop (scvi.inference.AdapterTrainer attribute)
(scvi.inference.AlternateSemiSupervisedTrainer attribute)
(scvi.inference.ClassifierTrainer attribute)
(scvi.inference.JVAETrainer attribute)
(scvi.inference.SemiSupervisedTrainer attribute)
(scvi.inference.Trainer attribute)
(scvi.inference.UnsupervisedTrainer attribute)
PreFrontalCortexStarmapDataset (class in scvi.dataset)
PurifiedPBMCDataset (class in scvi.dataset)
R
raw_counts_properties() (scvi.dataset.GeneExpressionDataset method)
raw_data() (scvi.inference.Posterior method)
reconstruction_error() (scvi.inference.Posterior method)
(scvi.inference.TotalPosterior method)
reconstruction_loss() (scvi.models.JVAE method)
register_dataset_version() (scvi.dataset.GeneExpressionDataset method)
register_posterior() (scvi.inference.Trainer method)
remap_categorical_attributes() (scvi.dataset.GeneExpressionDataset method)
reorder_cell_types() (scvi.dataset.GeneExpressionDataset method)
reorder_genes() (scvi.dataset.GeneExpressionDataset method)
reparameterize_gaussian() (in module scvi.models.modules)
reparameterize_transformation() (scvi.models.modules.EncoderTOTALVI method)
rescale_dropout() (scvi.models.AutoZIVAE method)
reshape_bernoulli() (scvi.models.AutoZIVAE method)
RetinaDataset (class in scvi.dataset)
S
sample_bernoulli_params() (scvi.models.AutoZIVAE method)
sample_from_beta_distribution() (scvi.models.AutoZIVAE method)
sample_from_posterior_l() (scvi.models.JVAE method)
(scvi.models.TOTALVI method)
(scvi.models.VAE method)
sample_from_posterior_z() (scvi.models.JVAE method)
(scvi.models.TOTALVI method)
(scvi.models.VAE method)
sample_rate() (scvi.models.JVAE method)
sample_scale() (scvi.models.JVAE method)
save_posterior() (scvi.inference.Posterior method)
scale_sampler() (scvi.inference.Posterior method)
SCANVI (class in scvi.models)
scvi.dataset
module
scvi.inference
module
scvi.models
module
scvi.models.modules
module
SemiSupervisedTrainer (class in scvi.inference)
SeqfishDataset (class in scvi.dataset)
SeqFishPlusDataset (class in scvi.dataset)
sequential() (scvi.inference.Posterior method)
show_t_sne() (scvi.inference.Posterior method)
SmfishDataset (class in scvi.dataset)
subsample_cells() (scvi.dataset.GeneExpressionDataset method)
subsample_genes() (scvi.dataset.GeneExpressionDataset method)
SyntheticDataset (class in scvi.dataset)
SyntheticDatasetCorr (class in scvi.dataset)
SyntheticRandomDataset (class in scvi.dataset)
T
to_anndata() (scvi.dataset.GeneExpressionDataset method)
to_cuda() (scvi.inference.Posterior method)
TotalPosterior (class in scvi.inference)
TotalTrainer (class in scvi.inference)
TOTALVI (class in scvi.models)
train() (scvi.inference.AdapterTrainer method)
(scvi.inference.TotalTrainer method)
(scvi.inference.Trainer method)
train_test_validation() (scvi.inference.Trainer method)
Trainer (class in scvi.inference)
training_extras_end() (scvi.inference.JVAETrainer method)
(scvi.inference.TotalTrainer method)
(scvi.inference.Trainer method)
training_extras_init() (scvi.inference.JVAETrainer method)
(scvi.inference.TotalTrainer method)
(scvi.inference.Trainer method)
U
uncorrupt_posteriors() (scvi.inference.Trainer method)
uncorrupted() (scvi.inference.Posterior method)
(scvi.inference.TotalPosterior method)
UnsupervisedTrainer (class in scvi.inference)
update() (scvi.inference.Posterior method)
update_cells() (scvi.dataset.GeneExpressionDataset method)
update_genes() (scvi.dataset.GeneExpressionDataset method)
update_sampler_indices() (scvi.inference.Posterior method)
V
VAE (class in scvi.models)
VAEC (class in scvi.models)
W
within_cluster_degenes() (scvi.inference.Posterior method)
X
X (scvi.dataset.GeneExpressionDataset attribute)
Z
ZISyntheticDatasetCorr (class in scvi.dataset)
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