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Index
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C
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D
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E
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F
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H
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I
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L
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M
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N
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Symbols
--doi
sfaira-annotate-dataloader command line option
sfaira-export-h5ad command line option
sfaira-finalize-dataloader command line option
sfaira-test-dataloader command line option
sfaira-validate-dataloader command line option
--h5ad
sfaira-validate-h5ad command line option
--log-file
sfaira command line option
--path-cache
sfaira-export-h5ad command line option
--path-data
sfaira-annotate-dataloader command line option
sfaira-create-dataloader command line option
sfaira-export-h5ad command line option
sfaira-finalize-dataloader command line option
sfaira-test-dataloader command line option
--path-loader
sfaira-annotate-dataloader command line option
sfaira-create-dataloader command line option
sfaira-export-h5ad command line option
sfaira-finalize-dataloader command line option
sfaira-test-dataloader command line option
sfaira-validate-dataloader command line option
--path-out
sfaira-export-h5ad command line option
--schema
sfaira-annotate-dataloader command line option
sfaira-export-h5ad command line option
sfaira-finalize-dataloader command line option
sfaira-test-dataloader command line option
sfaira-validate-dataloader command line option
sfaira-validate-h5ad command line option
--verbose
sfaira command line option
--version
sfaira command line option
-l
sfaira command line option
-v
sfaira command line option
A
acc_idx (sfaira.train.SummarizeGridsearchCelltype attribute)
adaptor() (sfaira.data.store.carts.CartMulti method)
(sfaira.data.store.carts.CartSingle method)
adata (sfaira.data.DatasetBase attribute)
(sfaira.data.DatasetGroup property)
(sfaira.data.DatasetGroupDirectoryOriented property)
(sfaira.data.DatasetSuperGroup property)
(sfaira.data.store.carts.CartMulti property)
(sfaira.data.store.carts.CartSingle property)
(sfaira.data.Universe property)
adata_by_key (sfaira.data.StoreMultipleFeatureSpaceBase property)
(sfaira.data.StoresAnndata property)
(sfaira.data.StoresDao property)
(sfaira.data.StoresH5ad property)
(sfaira.data.StoreSingleFeatureSpace property)
adata_ids (sfaira.ui.UserInterface attribute)
adata_ls (sfaira.data.DatasetGroup property)
(sfaira.data.DatasetGroupDirectoryOriented property)
(sfaira.data.DatasetSuperGroup property)
(sfaira.data.Universe property)
adata_memory_footprint (sfaira.data.StoreMultipleFeatureSpaceBase property)
(sfaira.data.StoresAnndata property)
(sfaira.data.StoresDao property)
(sfaira.data.StoresH5ad property)
(sfaira.data.StoreSingleFeatureSpace property)
add_extension() (sfaira.versions.metadata.OntologyCellosaurus method)
(sfaira.versions.metadata.OntologyCl method)
(sfaira.versions.metadata.OntologyHsapdv method)
(sfaira.versions.metadata.OntologyMmusdv method)
(sfaira.versions.metadata.OntologyMondo method)
(sfaira.versions.metadata.OntologyOboCustom method)
(sfaira.versions.metadata.OntologyUberon method)
additional_annotation_key (sfaira.data.DatasetBase property)
(sfaira.data.DatasetGroup property)
(sfaira.data.DatasetGroupDirectoryOriented property)
(sfaira.data.DatasetInteractive property)
(sfaira.data.DatasetSuperGroup property)
(sfaira.data.Universe property)
annotated (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
assay_differentiation (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
assay_differentiation_obs_key (sfaira.data.DatasetBase attribute)
assay_sc (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
assay_sc_obs_key (sfaira.data.DatasetBase attribute)
assay_type_differentiation (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
assay_type_differentiation_obs_key (sfaira.data.DatasetBase attribute)
author (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
B
batch_size (sfaira.data.store.carts.CartSingle attribute)
BatchDesignBalanced (class in sfaira.data.store.batch_schedule)
BatchDesignBase (class in sfaira.data.store.batch_schedule)
BatchDesignBasic (class in sfaira.data.store.batch_schedule)
BatchDesignBlocks (class in sfaira.data.store.batch_schedule)
BatchDesignFull (class in sfaira.data.store.batch_schedule)
batchsplits (sfaira.data.store.batch_schedule.BatchDesignBalanced property)
(sfaira.data.store.batch_schedule.BatchDesignBase property)
(sfaira.data.store.batch_schedule.BatchDesignBasic property)
(sfaira.data.store.batch_schedule.BatchDesignBlocks property)
(sfaira.data.store.batch_schedule.BatchDesignFull property)
best_model_by_partition() (sfaira.train.GridsearchContainer method)
(sfaira.train.SummarizeGridsearchCelltype method)
(sfaira.train.SummarizeGridsearchEmbedding method)
best_model_celltype() (sfaira.train.SummarizeGridsearchCelltype method)
best_model_embedding() (sfaira.train.SummarizeGridsearchEmbedding method)
bio_sample (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
bio_sample_obs_key (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
biotype (sfaira.versions.genomes.GenomeContainer property)
C
cache_fn (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
cache_path (sfaira.data.DatasetBase attribute)
(sfaira.estimators.EstimatorKeras attribute)
CartMulti (class in sfaira.data.store.carts)
carts (sfaira.data.store.carts.CartMulti attribute)
CartSingle (class in sfaira.data.store.carts)
cell_line (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
cell_type (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
cell_type_obs_key (sfaira.data.DatasetBase attribute)
celltype_summary() (sfaira.ui.UserInterface method)
celltype_universe (sfaira.estimators.EstimatorKerasCelltype attribute)
CellTypeMarker (class in sfaira.models.celltype)
CellTypeMlp (class in sfaira.models.celltype)
CellTypeMlpVersioned (class in sfaira.models.celltype)
celltypes_universe (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
CelltypeUniverse (class in sfaira.versions.metadata)
checkout() (sfaira.data.StoreMultipleFeatureSpaceBase method)
(sfaira.data.StoresAnndata method)
(sfaira.data.StoresDao method)
(sfaira.data.StoresH5ad method)
(sfaira.data.StoreSingleFeatureSpace method)
citation (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
clean_ontology_class_maps() (sfaira.data.DatasetGroupDirectoryOriented method)
clear() (sfaira.data.DatasetBase method)
(sfaira.data.DatasetInteractive method)
collapse_counts() (sfaira.data.DatasetBase method)
(sfaira.data.DatasetGroup method)
(sfaira.data.DatasetGroupDirectoryOriented method)
(sfaira.data.DatasetInteractive method)
(sfaira.data.DatasetSuperGroup method)
(sfaira.data.Universe method)
collection_id (sfaira.data.DatasetGroup property)
(sfaira.data.DatasetGroupDirectoryOriented property)
compute_denoised_expression() (sfaira.ui.UserInterface method)
compute_gradients_input() (sfaira.estimators.EstimatorKerasCelltype method)
(sfaira.estimators.EstimatorKerasEmbedding method)
convert_to_id() (sfaira.versions.metadata.OntologyCellosaurus method)
(sfaira.versions.metadata.OntologyCl method)
(sfaira.versions.metadata.OntologyHierarchical method)
(sfaira.versions.metadata.OntologyHsapdv method)
(sfaira.versions.metadata.OntologyList static method)
(sfaira.versions.metadata.OntologyMmusdv method)
(sfaira.versions.metadata.OntologyMondo method)
(sfaira.versions.metadata.OntologyObo method)
(sfaira.versions.metadata.OntologyOboCustom method)
(sfaira.versions.metadata.OntologyUberon method)
convert_to_name() (sfaira.versions.metadata.OntologyCellosaurus method)
(sfaira.versions.metadata.OntologyCl method)
(sfaira.versions.metadata.OntologyHierarchical method)
(sfaira.versions.metadata.OntologyHsapdv method)
(sfaira.versions.metadata.OntologyList static method)
(sfaira.versions.metadata.OntologyMmusdv method)
(sfaira.versions.metadata.OntologyMondo method)
(sfaira.versions.metadata.OntologyObo method)
(sfaira.versions.metadata.OntologyOboCustom method)
(sfaira.versions.metadata.OntologyUberon method)
create_summary_tab() (sfaira.train.SummarizeGridsearchCelltype method)
(sfaira.train.SummarizeGridsearchEmbedding method)
cv (sfaira.train.GridsearchContainer attribute)
cv_keys (sfaira.train.GridsearchContainer property)
(sfaira.train.SummarizeGridsearchCelltype property)
(sfaira.train.SummarizeGridsearchEmbedding property)
D
data (sfaira.estimators.EstimatorKeras attribute)
(sfaira.ui.UserInterface attribute)
data_by_key (sfaira.data.StoreMultipleFeatureSpaceBase property)
(sfaira.data.StoresAnndata property)
(sfaira.data.StoresDao property)
(sfaira.data.StoresH5ad property)
(sfaira.data.StoreSingleFeatureSpace property)
data_dir (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
data_dir_base (sfaira.data.DatasetBase attribute)
data_source (sfaira.data.StoreSingleFeatureSpace attribute)
dataset_groups (sfaira.data.DatasetSuperGroup attribute)
dataset_weights (sfaira.data.StoreSingleFeatureSpace property)
DatasetBase (class in sfaira.data)
DatasetGroup (class in sfaira.data)
DatasetGroupDirectoryOriented (class in sfaira.data)
DatasetInteractive (class in sfaira.data)
datasets (sfaira.data.DatasetGroup attribute)
(sfaira.data.DatasetSuperGroup property)
(sfaira.data.Universe property)
DatasetSuperGroup (class in sfaira.data)
default_embedding (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
deposit_zenodo() (sfaira.ui.UserInterface method)
design (sfaira.data.store.batch_schedule.BatchDesignBalanced property)
(sfaira.data.store.batch_schedule.BatchDesignBase property)
(sfaira.data.store.batch_schedule.BatchDesignBasic property)
(sfaira.data.store.batch_schedule.BatchDesignBlocks property)
(sfaira.data.store.batch_schedule.BatchDesignFull property)
development_stage (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
development_stage_obs_key (sfaira.data.DatasetBase attribute)
directory_formatted_doi (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
disease (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
disease_obs_key (sfaira.data.DatasetBase attribute)
doi (sfaira.data.DatasetBase property)
(sfaira.data.DatasetGroup property)
(sfaira.data.DatasetGroupDirectoryOriented property)
(sfaira.data.DatasetInteractive property)
doi_cleaned_id (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
doi_journal (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
doi_main (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
doi_preprint (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
download() (sfaira.data.DatasetBase method)
(sfaira.data.DatasetGroup method)
(sfaira.data.DatasetGroupDirectoryOriented method)
(sfaira.data.DatasetInteractive method)
(sfaira.data.DatasetSuperGroup method)
(sfaira.data.Universe method)
download_url_data (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
download_url_meta (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
E
ensembl (sfaira.versions.genomes.GenomeContainer property)
estimator (sfaira.train.TrainModelCelltype attribute)
(sfaira.train.TrainModelEmbedding attribute)
estimator_celltype (sfaira.ui.UserInterface attribute)
estimator_embedding (sfaira.ui.UserInterface attribute)
EstimatorKeras (class in sfaira.estimators)
EstimatorKerasCelltype (class in sfaira.estimators)
EstimatorKerasEmbedding (class in sfaira.estimators)
ethnicity (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
ethnicity_obs_key (sfaira.data.DatasetBase attribute)
evals (sfaira.train.GridsearchContainer attribute)
evaluate() (sfaira.estimators.EstimatorKerasCelltype method)
(sfaira.estimators.EstimatorKerasEmbedding method)
evaluate_any() (sfaira.estimators.EstimatorKerasCelltype method)
(sfaira.estimators.EstimatorKerasEmbedding method)
extend_dataset_groups() (sfaira.data.DatasetSuperGroup method)
(sfaira.data.Universe method)
F
feature_id_var_key (sfaira.data.DatasetBase attribute)
feature_reference (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
feature_reference_var_key (sfaira.data.DatasetBase attribute)
feature_symbol_var_key (sfaira.data.DatasetBase attribute)
feature_type (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
feature_type_var_key (sfaira.data.DatasetBase attribute)
flatten() (sfaira.data.DatasetSuperGroup method)
(sfaira.data.Universe method)
fn_backed (sfaira.data.DatasetSuperGroup attribute)
G
genome (sfaira.data.DatasetBase attribute)
genome_container (sfaira.data.StoreMultipleFeatureSpaceBase property)
(sfaira.data.StoresAnndata property)
(sfaira.data.StoresDao property)
(sfaira.data.StoresH5ad property)
(sfaira.data.StoreSingleFeatureSpace property)
genome_tab (sfaira.versions.genomes.GenomeContainer attribute)
GenomeContainer (class in sfaira.versions.genomes)
get_ancestors() (sfaira.versions.metadata.OntologyCellosaurus method)
(sfaira.versions.metadata.OntologyCl method)
(sfaira.versions.metadata.OntologyHierarchical method)
(sfaira.versions.metadata.OntologyHsapdv method)
(sfaira.versions.metadata.OntologyList method)
(sfaira.versions.metadata.OntologyMmusdv method)
(sfaira.versions.metadata.OntologyMondo method)
(sfaira.versions.metadata.OntologyObo method)
(sfaira.versions.metadata.OntologyOboCustom method)
(sfaira.versions.metadata.OntologyUberon method)
get_best_model_ids() (sfaira.train.GridsearchContainer method)
(sfaira.train.SummarizeGridsearchCelltype method)
(sfaira.train.SummarizeGridsearchEmbedding method)
get_descendants() (sfaira.versions.metadata.OntologyCellosaurus method)
(sfaira.versions.metadata.OntologyCl method)
(sfaira.versions.metadata.OntologyHierarchical method)
(sfaira.versions.metadata.OntologyHsapdv method)
(sfaira.versions.metadata.OntologyMmusdv method)
(sfaira.versions.metadata.OntologyMondo method)
(sfaira.versions.metadata.OntologyObo method)
(sfaira.versions.metadata.OntologyOboCustom method)
(sfaira.versions.metadata.OntologyUberon method)
get_effective_leaves() (sfaira.versions.metadata.OntologyCellosaurus method)
(sfaira.versions.metadata.OntologyCl method)
(sfaira.versions.metadata.OntologyHierarchical method)
(sfaira.versions.metadata.OntologyHsapdv method)
(sfaira.versions.metadata.OntologyMmusdv method)
(sfaira.versions.metadata.OntologyMondo method)
(sfaira.versions.metadata.OntologyObo method)
(sfaira.versions.metadata.OntologyOboCustom method)
(sfaira.versions.metadata.OntologyUberon method)
get_gc() (sfaira.data.DatasetSuperGroup method)
(sfaira.data.Universe method)
get_gradients_by_celltype() (sfaira.train.SummarizeGridsearchEmbedding method)
get_one_time_tf_dataset() (sfaira.estimators.EstimatorKeras method)
(sfaira.estimators.EstimatorKerasCelltype method)
(sfaira.estimators.EstimatorKerasEmbedding method)
get_ontology() (sfaira.data.DatasetBase method)
(sfaira.data.DatasetInteractive method)
get_subset_idx() (sfaira.data.StoreSingleFeatureSpace method)
gm (sfaira.data.DatasetBase attribute)
gm_obs_key (sfaira.data.DatasetBase attribute)
graph (sfaira.versions.metadata.OntologyCellosaurus property)
(sfaira.versions.metadata.OntologyCl property)
(sfaira.versions.metadata.OntologyHierarchical property)
(sfaira.versions.metadata.OntologyHsapdv property)
(sfaira.versions.metadata.OntologyMmusdv property)
(sfaira.versions.metadata.OntologyMondo property)
(sfaira.versions.metadata.OntologyObo property)
(sfaira.versions.metadata.OntologyOboCustom property)
(sfaira.versions.metadata.OntologyUberon property)
GridsearchContainer (class in sfaira.train)
grouping (sfaira.data.store.batch_schedule.BatchDesignBlocks property)
groups (sfaira.data.store.batch_schedule.BatchDesignBlocks property)
gs_keys (sfaira.train.GridsearchContainer attribute)
H
histories (sfaira.train.GridsearchContainer attribute)
history (sfaira.estimators.EstimatorKeras attribute)
I
id (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
id_to_symbols_dict (sfaira.versions.genomes.GenomeContainer property)
ids (sfaira.data.DatasetGroup property)
(sfaira.data.DatasetGroupDirectoryOriented property)
(sfaira.data.DatasetSuperGroup property)
(sfaira.data.Universe property)
idx (sfaira.data.store.batch_schedule.BatchDesignBalanced property)
(sfaira.data.store.batch_schedule.BatchDesignBase property)
(sfaira.data.store.batch_schedule.BatchDesignBasic property)
(sfaira.data.store.batch_schedule.BatchDesignBlocks property)
(sfaira.data.store.batch_schedule.BatchDesignFull property)
(sfaira.data.StoreSingleFeatureSpace property)
idx_eval (sfaira.estimators.EstimatorKeras attribute)
idx_test (sfaira.estimators.EstimatorKeras attribute)
idx_train (sfaira.estimators.EstimatorKeras attribute)
indices (sfaira.data.StoreMultipleFeatureSpaceBase property)
(sfaira.data.StoresAnndata property)
(sfaira.data.StoresDao property)
(sfaira.data.StoresH5ad property)
(sfaira.data.StoreSingleFeatureSpace property)
individual (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
individual_obs_key (sfaira.data.DatasetBase attribute)
init_estim() (sfaira.train.TrainModelCelltype method)
(sfaira.train.TrainModelEmbedding method)
init_model() (sfaira.estimators.EstimatorKeras method)
(sfaira.estimators.EstimatorKerasCelltype method)
(sfaira.estimators.EstimatorKerasEmbedding method)
intercalated (sfaira.data.store.carts.CartMulti attribute)
is_a() (sfaira.versions.metadata.OntologyCellosaurus method)
(sfaira.versions.metadata.OntologyCl method)
(sfaira.versions.metadata.OntologyHierarchical method)
(sfaira.versions.metadata.OntologyHsapdv method)
(sfaira.versions.metadata.OntologyList method)
(sfaira.versions.metadata.OntologyMmusdv method)
(sfaira.versions.metadata.OntologyMondo method)
(sfaira.versions.metadata.OntologyObo method)
(sfaira.versions.metadata.OntologyOboCustom method)
(sfaira.versions.metadata.OntologyUberon method)
is_a_node_id() (sfaira.versions.metadata.OntologyCellosaurus method)
(sfaira.versions.metadata.OntologyCl method)
(sfaira.versions.metadata.OntologyHierarchical method)
(sfaira.versions.metadata.OntologyHsapdv method)
(sfaira.versions.metadata.OntologyList method)
(sfaira.versions.metadata.OntologyMmusdv method)
(sfaira.versions.metadata.OntologyMondo method)
(sfaira.versions.metadata.OntologyObo method)
(sfaira.versions.metadata.OntologyOboCustom method)
(sfaira.versions.metadata.OntologyUberon method)
is_a_node_name() (sfaira.versions.metadata.OntologyCellosaurus method)
(sfaira.versions.metadata.OntologyCl method)
(sfaira.versions.metadata.OntologyHierarchical method)
(sfaira.versions.metadata.OntologyHsapdv method)
(sfaira.versions.metadata.OntologyList method)
(sfaira.versions.metadata.OntologyMmusdv method)
(sfaira.versions.metadata.OntologyMondo method)
(sfaira.versions.metadata.OntologyObo method)
(sfaira.versions.metadata.OntologyOboCustom method)
(sfaira.versions.metadata.OntologyUberon method)
is_node() (sfaira.versions.metadata.Ontology method)
(sfaira.versions.metadata.OntologyCellosaurus method)
(sfaira.versions.metadata.OntologyCl method)
(sfaira.versions.metadata.OntologyHierarchical method)
(sfaira.versions.metadata.OntologyHsapdv method)
(sfaira.versions.metadata.OntologyList method)
(sfaira.versions.metadata.OntologyMmusdv method)
(sfaira.versions.metadata.OntologyMondo method)
(sfaira.versions.metadata.OntologyObo method)
(sfaira.versions.metadata.OntologyOboCustom method)
(sfaira.versions.metadata.OntologyUberon method)
iterator() (sfaira.data.store.carts.CartMulti method)
(sfaira.data.store.carts.CartSingle method)
L
layer_counts (sfaira.data.DatasetBase attribute)
layer_processed (sfaira.data.DatasetBase attribute)
layer_spliced_counts (sfaira.data.DatasetBase attribute)
layer_spliced_processed (sfaira.data.DatasetBase attribute)
layer_unspliced_counts (sfaira.data.DatasetBase attribute)
layer_unspliced_processed (sfaira.data.DatasetBase attribute)
layer_velocity (sfaira.data.DatasetBase attribute)
leaves (sfaira.versions.metadata.Ontology attribute)
(sfaira.versions.metadata.OntologyCellosaurus property)
(sfaira.versions.metadata.OntologyCl property)
(sfaira.versions.metadata.OntologyHierarchical property)
(sfaira.versions.metadata.OntologyHsapdv property)
(sfaira.versions.metadata.OntologyList property)
(sfaira.versions.metadata.OntologyMmusdv property)
(sfaira.versions.metadata.OntologyMondo property)
(sfaira.versions.metadata.OntologyObo property)
(sfaira.versions.metadata.OntologyOboCustom property)
(sfaira.versions.metadata.OntologyUberon property)
List (sfaira.train.SummarizeGridsearchEmbedding attribute)
load() (sfaira.data.DatasetBase method)
(sfaira.data.DatasetGroup method)
(sfaira.data.DatasetGroupDirectoryOriented method)
(sfaira.data.DatasetInteractive method)
(sfaira.data.DatasetSuperGroup method)
(sfaira.data.Universe method)
load_config() (sfaira.data.DatasetSuperGroup method)
(sfaira.data.StoreMultipleFeatureSpaceBase method)
(sfaira.data.StoresAnndata method)
(sfaira.data.StoresDao method)
(sfaira.data.StoresH5ad method)
(sfaira.data.StoreSingleFeatureSpace method)
(sfaira.data.Universe method)
load_data() (sfaira.ui.UserInterface method)
load_genome() (sfaira.versions.genomes.GenomeContainer method)
load_gs() (sfaira.train.GridsearchContainer method)
(sfaira.train.SummarizeGridsearchCelltype method)
(sfaira.train.SummarizeGridsearchEmbedding method)
load_into_memory() (sfaira.train.TrainModelCelltype method)
(sfaira.train.TrainModelEmbedding method)
load_meta() (sfaira.data.DatasetBase method)
(sfaira.data.DatasetInteractive method)
load_model_celltype() (sfaira.ui.UserInterface method)
load_model_embedding() (sfaira.ui.UserInterface method)
load_ontology_names() (sfaira.train.SummarizeGridsearchCelltype method)
load_pretrained_weights() (sfaira.estimators.EstimatorKeras method)
(sfaira.estimators.EstimatorKerasCelltype method)
(sfaira.estimators.EstimatorKerasEmbedding method)
load_raw (sfaira.data.DatasetBase attribute)
load_store() (in module sfaira.data)
load_target_universe() (sfaira.versions.metadata.CelltypeUniverse method)
load_weights_from_cache() (sfaira.estimators.EstimatorKeras method)
(sfaira.estimators.EstimatorKerasCelltype method)
(sfaira.estimators.EstimatorKerasEmbedding method)
load_y() (sfaira.train.GridsearchContainer method)
(sfaira.train.SummarizeGridsearchCelltype method)
(sfaira.train.SummarizeGridsearchEmbedding method)
loaded (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
loss_idx (sfaira.train.SummarizeGridsearchCelltype attribute)
(sfaira.train.SummarizeGridsearchEmbedding attribute)
M
map_node_suggestion() (sfaira.versions.metadata.Ontology method)
(sfaira.versions.metadata.OntologyCellosaurus method)
(sfaira.versions.metadata.OntologyCl method)
(sfaira.versions.metadata.OntologyHierarchical method)
(sfaira.versions.metadata.OntologyHsapdv method)
(sfaira.versions.metadata.OntologyList method)
(sfaira.versions.metadata.OntologyMmusdv method)
(sfaira.versions.metadata.OntologyMondo method)
(sfaira.versions.metadata.OntologyObo method)
(sfaira.versions.metadata.OntologyOboCustom method)
(sfaira.versions.metadata.OntologyUberon method)
map_to_leaves() (sfaira.versions.metadata.OntologyCellosaurus method)
(sfaira.versions.metadata.OntologyCl method)
(sfaira.versions.metadata.OntologyHierarchical method)
(sfaira.versions.metadata.OntologyHsapdv method)
(sfaira.versions.metadata.OntologyMmusdv method)
(sfaira.versions.metadata.OntologyMondo method)
(sfaira.versions.metadata.OntologyObo method)
(sfaira.versions.metadata.OntologyOboCustom method)
(sfaira.versions.metadata.OntologyUberon method)
mapped_features (sfaira.data.DatasetBase attribute)
md5 (sfaira.estimators.EstimatorKeras attribute)
meta (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
meta_fn (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
meta_path (sfaira.data.DatasetBase attribute)
model (sfaira.estimators.EstimatorKeras attribute)
(sfaira.estimators.EstimatorKerasCelltype attribute)
(sfaira.estimators.EstimatorKerasEmbedding attribute)
model_dir (sfaira.estimators.EstimatorKeras attribute)
model_id (sfaira.estimators.EstimatorKeras attribute)
model_id_len (sfaira.train.GridsearchContainer attribute)
model_lookuptable (sfaira.ui.UserInterface attribute)
model_type (sfaira.estimators.EstimatorKerasCelltype property)
(sfaira.estimators.EstimatorKerasEmbedding property)
(sfaira.versions.topologies.TopologyContainer property)
ModelAeVersioned (class in sfaira.models.embedding)
ModelKerasAe (class in sfaira.models.embedding)
ModelKerasLinear (class in sfaira.models.embedding)
ModelKerasVae (class in sfaira.models.embedding)
ModelKerasVaeIAF (class in sfaira.models.embedding)
ModelKerasVaeVamp (class in sfaira.models.embedding)
ModelLinearVersioned (class in sfaira.models.embedding)
ModelVaeIAFVersioned (class in sfaira.models.embedding)
ModelVaeVampVersioned (class in sfaira.models.embedding)
ModelVaeVersioned (class in sfaira.models.embedding)
module
sfaira.data
,
[1]
,
[2]
sfaira.estimators
sfaira.models
sfaira.train
sfaira.ui
sfaira.versions
move_to_memory() (sfaira.data.store.carts.CartMulti method)
(sfaira.data.store.carts.CartSingle method)
mse_idx (sfaira.train.SummarizeGridsearchEmbedding attribute)
N
n_batches (sfaira.data.store.batch_schedule.BatchDesignBalanced property)
(sfaira.data.store.batch_schedule.BatchDesignBase property)
(sfaira.data.store.batch_schedule.BatchDesignBasic property)
(sfaira.data.store.batch_schedule.BatchDesignBlocks property)
(sfaira.data.store.batch_schedule.BatchDesignFull property)
(sfaira.data.store.carts.CartMulti property)
(sfaira.data.store.carts.CartSingle property)
n_counts() (sfaira.train.TrainModelCelltype method)
(sfaira.train.TrainModelEmbedding method)
n_leaves (sfaira.versions.metadata.OntologyCellosaurus property)
(sfaira.versions.metadata.OntologyCl property)
(sfaira.versions.metadata.OntologyHierarchical property)
(sfaira.versions.metadata.OntologyHsapdv property)
(sfaira.versions.metadata.OntologyList property)
(sfaira.versions.metadata.OntologyMmusdv property)
(sfaira.versions.metadata.OntologyMondo property)
(sfaira.versions.metadata.OntologyObo property)
(sfaira.versions.metadata.OntologyOboCustom property)
(sfaira.versions.metadata.OntologyUberon property)
n_obs (sfaira.data.store.carts.CartMulti property)
(sfaira.data.store.carts.CartSingle property)
(sfaira.data.StoreMultipleFeatureSpaceBase property)
(sfaira.data.StoresAnndata property)
(sfaira.data.StoresDao property)
(sfaira.data.StoresH5ad property)
(sfaira.data.StoreSingleFeatureSpace property)
n_obs_dict (sfaira.data.StoreMultipleFeatureSpaceBase property)
(sfaira.data.StoresAnndata property)
(sfaira.data.StoresDao property)
(sfaira.data.StoresH5ad property)
n_obs_selected (sfaira.data.store.carts.CartMulti property)
(sfaira.data.store.carts.CartSingle property)
n_var (sfaira.data.store.carts.CartMulti property)
(sfaira.data.store.carts.CartSingle property)
(sfaira.versions.genomes.GenomeContainer property)
(sfaira.versions.topologies.TopologyContainer property)
n_vars (sfaira.data.StoreMultipleFeatureSpaceBase property)
(sfaira.data.StoresAnndata property)
(sfaira.data.StoresDao property)
(sfaira.data.StoresH5ad property)
(sfaira.data.StoreSingleFeatureSpace property)
ncells (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
ncells() (sfaira.data.DatasetGroup method)
(sfaira.data.DatasetGroupDirectoryOriented method)
(sfaira.data.DatasetSuperGroup method)
(sfaira.data.Universe method)
ncells_bydataset() (sfaira.data.DatasetGroup method)
(sfaira.data.DatasetGroupDirectoryOriented method)
(sfaira.data.DatasetSuperGroup method)
(sfaira.data.Universe method)
ncells_bydataset_flat() (sfaira.data.DatasetSuperGroup method)
(sfaira.data.Universe method)
node_ids (sfaira.versions.metadata.OntologyCellosaurus property)
(sfaira.versions.metadata.OntologyCl property)
(sfaira.versions.metadata.OntologyHierarchical property)
(sfaira.versions.metadata.OntologyHsapdv property)
(sfaira.versions.metadata.OntologyList property)
(sfaira.versions.metadata.OntologyMmusdv property)
(sfaira.versions.metadata.OntologyMondo property)
(sfaira.versions.metadata.OntologyObo property)
(sfaira.versions.metadata.OntologyOboCustom property)
(sfaira.versions.metadata.OntologyUberon property)
node_names (sfaira.versions.metadata.OntologyCellosaurus property)
(sfaira.versions.metadata.OntologyCl property)
(sfaira.versions.metadata.OntologyHierarchical property)
(sfaira.versions.metadata.OntologyHsapdv property)
(sfaira.versions.metadata.OntologyList property)
(sfaira.versions.metadata.OntologyMmusdv property)
(sfaira.versions.metadata.OntologyMondo property)
(sfaira.versions.metadata.OntologyObo property)
(sfaira.versions.metadata.OntologyOboCustom property)
(sfaira.versions.metadata.OntologyUberon property)
node_names() (sfaira.versions.metadata.Ontology method)
nodes (sfaira.versions.metadata.OntologyCellosaurus property)
(sfaira.versions.metadata.OntologyCl property)
(sfaira.versions.metadata.OntologyHierarchical property)
(sfaira.versions.metadata.OntologyHsapdv property)
(sfaira.versions.metadata.OntologyList attribute)
(sfaira.versions.metadata.OntologyMmusdv property)
(sfaira.versions.metadata.OntologyMondo property)
(sfaira.versions.metadata.OntologyObo property)
(sfaira.versions.metadata.OntologyOboCustom property)
(sfaira.versions.metadata.OntologyUberon property)
nodes_dict (sfaira.versions.metadata.OntologyCellosaurus property)
(sfaira.versions.metadata.OntologyCl property)
(sfaira.versions.metadata.OntologyHierarchical property)
(sfaira.versions.metadata.OntologyHsapdv property)
(sfaira.versions.metadata.OntologyMmusdv property)
(sfaira.versions.metadata.OntologyMondo property)
(sfaira.versions.metadata.OntologyObo property)
(sfaira.versions.metadata.OntologyOboCustom property)
(sfaira.versions.metadata.OntologyUberon property)
ntypes (sfaira.estimators.EstimatorKerasCelltype property)
O
obs (sfaira.data.store.carts.CartMulti property)
(sfaira.data.store.carts.CartSingle property)
(sfaira.estimators.EstimatorKerasCelltype property)
(sfaira.estimators.EstimatorKerasEmbedding property)
obs_by_key (sfaira.data.StoreMultipleFeatureSpaceBase property)
(sfaira.data.StoresAnndata property)
(sfaira.data.StoresDao property)
(sfaira.data.StoresH5ad property)
(sfaira.data.StoreSingleFeatureSpace property)
obs_concat() (sfaira.data.DatasetGroup method)
(sfaira.data.DatasetGroupDirectoryOriented method)
obs_eval (sfaira.estimators.EstimatorKerasCelltype property)
(sfaira.estimators.EstimatorKerasEmbedding property)
obs_idx (sfaira.data.store.carts.CartMulti property)
(sfaira.data.store.carts.CartSingle property)
obs_keys (sfaira.data.store.carts.CartSingle attribute)
obs_test (sfaira.estimators.EstimatorKerasCelltype property)
(sfaira.estimators.EstimatorKerasEmbedding property)
obs_train (sfaira.estimators.EstimatorKerasCelltype property)
(sfaira.estimators.EstimatorKerasEmbedding property)
onto_cl (sfaira.versions.metadata.CelltypeUniverse attribute)
onto_uberon (sfaira.versions.metadata.CelltypeUniverse attribute)
Ontology (class in sfaira.versions.metadata)
ontology_celltypes (sfaira.data.DatasetGroup property)
(sfaira.data.DatasetGroupDirectoryOriented property)
ontology_class_maps (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
ontology_container_sfaira (sfaira.data.DatasetGroup property)
(sfaira.data.DatasetGroupDirectoryOriented property)
ontology_ids (sfaira.estimators.EstimatorKerasCelltype property)
ontology_names (sfaira.estimators.EstimatorKerasCelltype property)
OntologyCellosaurus (class in sfaira.versions.metadata)
OntologyCl (class in sfaira.versions.metadata)
OntologyHierarchical (class in sfaira.versions.metadata)
OntologyHsapdv (class in sfaira.versions.metadata)
OntologyList (class in sfaira.versions.metadata)
OntologyMmusdv (class in sfaira.versions.metadata)
OntologyMondo (class in sfaira.versions.metadata)
OntologyObo (class in sfaira.versions.metadata)
OntologyOboCustom (class in sfaira.versions.metadata)
OntologyUberon (class in sfaira.versions.metadata)
organ (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
organ_obs_key (sfaira.data.DatasetBase attribute)
organism (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
(sfaira.data.StoreSingleFeatureSpace property)
(sfaira.estimators.EstimatorKerasCelltype property)
(sfaira.estimators.EstimatorKerasEmbedding property)
(sfaira.versions.topologies.TopologyContainer property)
organism() (sfaira.versions.genomes.GenomeContainer method)
organism_obs_key (sfaira.data.DatasetBase attribute)
organisms_by_key (sfaira.data.StoreSingleFeatureSpace property)
output (sfaira.versions.topologies.TopologyContainer property)
P
plot_active_latent_units() (sfaira.train.SummarizeGridsearchEmbedding method)
plot_best() (sfaira.train.SummarizeGridsearchCelltype method)
(sfaira.train.SummarizeGridsearchEmbedding method)
plot_best_classwise_heatmap() (sfaira.train.SummarizeGridsearchCelltype method)
plot_best_classwise_scatter() (sfaira.train.SummarizeGridsearchCelltype method)
plot_best_model_by_hyperparam() (sfaira.train.GridsearchContainer method)
(sfaira.train.SummarizeGridsearchCelltype method)
(sfaira.train.SummarizeGridsearchEmbedding method)
plot_completions() (sfaira.train.GridsearchContainer method)
(sfaira.train.SummarizeGridsearchCelltype method)
(sfaira.train.SummarizeGridsearchEmbedding method)
plot_gradient_cor() (sfaira.train.SummarizeGridsearchEmbedding method)
plot_gradient_distr() (sfaira.train.SummarizeGridsearchEmbedding method)
plot_npc() (sfaira.train.SummarizeGridsearchEmbedding method)
plot_training_history() (sfaira.train.GridsearchContainer method)
(sfaira.train.SummarizeGridsearchCelltype method)
(sfaira.train.SummarizeGridsearchEmbedding method)
predict() (sfaira.estimators.EstimatorKerasCelltype method)
(sfaira.estimators.EstimatorKerasEmbedding method)
(sfaira.models.celltype.CellTypeMarker method)
(sfaira.models.celltype.CellTypeMlp method)
(sfaira.models.celltype.CellTypeMlpVersioned method)
predict_all() (sfaira.ui.UserInterface method)
predict_celltypes() (sfaira.ui.UserInterface method)
predict_embedding() (sfaira.estimators.EstimatorKerasEmbedding method)
(sfaira.models.embedding.ModelAeVersioned method)
(sfaira.models.embedding.ModelKerasAe method)
(sfaira.models.embedding.ModelKerasLinear method)
(sfaira.models.embedding.ModelKerasVae method)
(sfaira.models.embedding.ModelKerasVaeIAF method)
(sfaira.models.embedding.ModelKerasVaeVamp method)
(sfaira.models.embedding.ModelLinearVersioned method)
(sfaira.models.embedding.ModelVaeIAFVersioned method)
(sfaira.models.embedding.ModelVaeVampVersioned method)
(sfaira.models.embedding.ModelVaeVersioned method)
(sfaira.ui.UserInterface method)
predict_reconstructed() (sfaira.models.embedding.ModelAeVersioned method)
(sfaira.models.embedding.ModelKerasAe method)
(sfaira.models.embedding.ModelKerasLinear method)
(sfaira.models.embedding.ModelKerasVae method)
(sfaira.models.embedding.ModelKerasVaeIAF method)
(sfaira.models.embedding.ModelKerasVaeVamp method)
(sfaira.models.embedding.ModelLinearVersioned method)
(sfaira.models.embedding.ModelVaeIAFVersioned method)
(sfaira.models.embedding.ModelVaeVampVersioned method)
(sfaira.models.embedding.ModelVaeVersioned method)
prepare_maps_to_leaves() (sfaira.versions.metadata.OntologyCellosaurus method)
(sfaira.versions.metadata.OntologyCl method)
(sfaira.versions.metadata.OntologyHierarchical method)
(sfaira.versions.metadata.OntologyHsapdv method)
(sfaira.versions.metadata.OntologyList method)
(sfaira.versions.metadata.OntologyMmusdv method)
(sfaira.versions.metadata.OntologyMondo method)
(sfaira.versions.metadata.OntologyObo method)
(sfaira.versions.metadata.OntologyOboCustom method)
(sfaira.versions.metadata.OntologyUberon method)
primary_data (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
project_celltypes_to_ontology() (sfaira.data.DatasetGroup method)
(sfaira.data.DatasetGroupDirectoryOriented method)
(sfaira.data.DatasetSuperGroup method)
(sfaira.data.Universe method)
project_free_to_ontology() (sfaira.data.DatasetBase method)
(sfaira.data.DatasetInteractive method)
R
ratios (sfaira.data.store.carts.CartMulti property)
read_ontology_class_maps() (sfaira.data.DatasetBase method)
(sfaira.data.DatasetInteractive method)
release (sfaira.versions.genomes.GenomeContainer attribute)
remove_duplicates() (sfaira.data.DatasetSuperGroup method)
(sfaira.data.Universe method)
remove_gene_version (sfaira.data.DatasetBase attribute)
reset_root() (sfaira.versions.metadata.OntologyCellosaurus method)
(sfaira.versions.metadata.OntologyCl method)
(sfaira.versions.metadata.OntologyHierarchical method)
(sfaira.versions.metadata.OntologyHsapdv method)
(sfaira.versions.metadata.OntologyMmusdv method)
(sfaira.versions.metadata.OntologyMondo method)
(sfaira.versions.metadata.OntologyObo method)
(sfaira.versions.metadata.OntologyOboCustom method)
(sfaira.versions.metadata.OntologyUberon method)
run_ids (sfaira.train.GridsearchContainer attribute)
S
sample_fn (sfaira.data.DatasetBase attribute)
sample_source (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
sample_source_obs_key (sfaira.data.DatasetBase attribute)
save() (sfaira.train.TrainModelCelltype method)
(sfaira.train.TrainModelEmbedding method)
save_best_weight() (sfaira.train.GridsearchContainer method)
(sfaira.train.SummarizeGridsearchCelltype method)
(sfaira.train.SummarizeGridsearchEmbedding method)
save_eval() (sfaira.train.TrainModelCelltype method)
(sfaira.train.TrainModelEmbedding method)
save_weights_to_cache() (sfaira.estimators.EstimatorKeras method)
(sfaira.estimators.EstimatorKerasCelltype method)
(sfaira.estimators.EstimatorKerasEmbedding method)
schedule (sfaira.data.store.carts.CartSingle attribute)
set() (sfaira.versions.genomes.GenomeContainer method)
set_dataset_groups() (sfaira.data.DatasetSuperGroup method)
(sfaira.data.Universe method)
set_dataset_id() (sfaira.data.DatasetBase method)
(sfaira.data.DatasetInteractive method)
sex (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
sex_obs_key (sfaira.data.DatasetBase attribute)
sfaira command line option
--log-file
--verbose
--version
-l
-v
sfaira-annotate-dataloader command line option
--doi
--path-data
--path-loader
--schema
sfaira-create-dataloader command line option
--path-data
--path-loader
sfaira-export-h5ad command line option
--doi
--path-cache
--path-data
--path-loader
--path-out
--schema
sfaira-finalize-dataloader command line option
--doi
--path-data
--path-loader
--schema
sfaira-test-dataloader command line option
--doi
--path-data
--path-loader
--schema
sfaira-validate-dataloader command line option
--doi
--path-loader
--schema
sfaira-validate-h5ad command line option
--h5ad
--schema
sfaira.data
module
,
[1]
,
[2]
sfaira.estimators
module
sfaira.models
module
sfaira.train
module
sfaira.ui
module
sfaira.versions
module
shape (sfaira.data.StoreMultipleFeatureSpaceBase property)
(sfaira.data.StoresAnndata property)
(sfaira.data.StoresDao property)
(sfaira.data.StoresH5ad property)
(sfaira.data.StoreSingleFeatureSpace property)
show_summary() (sfaira.data.DatasetBase method)
(sfaira.data.DatasetGroup method)
(sfaira.data.DatasetGroupDirectoryOriented method)
(sfaira.data.DatasetInteractive method)
(sfaira.data.DatasetSuperGroup method)
(sfaira.data.Universe method)
source (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
source_doi (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
source_doi_obs_key (sfaira.data.DatasetBase attribute)
source_path (sfaira.train.GridsearchContainer attribute)
spatial_x_coord_obs_key (sfaira.data.DatasetBase attribute)
spatial_y_coord_obs_key (sfaira.data.DatasetBase attribute)
spatial_z_coord_obs_key (sfaira.data.DatasetBase attribute)
split_train_val_test() (sfaira.estimators.EstimatorKeras method)
(sfaira.estimators.EstimatorKerasCelltype method)
(sfaira.estimators.EstimatorKerasEmbedding method)
state_exact (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
state_exact_obs_key (sfaira.data.DatasetBase attribute)
StoreMultipleFeatureSpaceBase (class in sfaira.data)
stores (sfaira.data.StoreMultipleFeatureSpaceBase property)
(sfaira.data.StoresAnndata property)
(sfaira.data.StoresDao property)
(sfaira.data.StoresH5ad property)
StoresAnndata (class in sfaira.data)
StoresDao (class in sfaira.data)
StoresH5ad (class in sfaira.data)
StoreSingleFeatureSpace (class in sfaira.data)
streamline_features() (sfaira.data.DatasetBase method)
(sfaira.data.DatasetGroup method)
(sfaira.data.DatasetGroupDirectoryOriented method)
(sfaira.data.DatasetInteractive method)
(sfaira.data.DatasetSuperGroup method)
(sfaira.data.Universe method)
streamline_metadata() (sfaira.data.DatasetBase method)
(sfaira.data.DatasetGroup method)
(sfaira.data.DatasetGroupDirectoryOriented method)
(sfaira.data.DatasetInteractive method)
(sfaira.data.DatasetSuperGroup method)
(sfaira.data.Universe method)
streamlined_meta (sfaira.data.DatasetBase attribute)
strippednames_to_id_dict (sfaira.versions.genomes.GenomeContainer property)
subset() (sfaira.data.DatasetGroup method)
(sfaira.data.DatasetGroupDirectoryOriented method)
(sfaira.data.DatasetSuperGroup method)
(sfaira.data.StoreMultipleFeatureSpaceBase method)
(sfaira.data.StoresAnndata method)
(sfaira.data.StoresDao method)
(sfaira.data.StoresH5ad method)
(sfaira.data.StoreSingleFeatureSpace method)
(sfaira.data.Universe method)
subset_cells() (sfaira.data.DatasetBase method)
(sfaira.data.DatasetGroup method)
(sfaira.data.DatasetGroupDirectoryOriented method)
(sfaira.data.DatasetInteractive method)
(sfaira.data.DatasetSuperGroup method)
(sfaira.data.Universe method)
subset_gene_type (sfaira.data.DatasetBase attribute)
SummarizeGridsearchCelltype (class in sfaira.train)
SummarizeGridsearchEmbedding (class in sfaira.train)
summary_tab (sfaira.train.GridsearchContainer attribute)
supplier (sfaira.data.DatasetBase attribute)
(sfaira.data.DatasetGroup property)
(sfaira.data.DatasetGroupDirectoryOriented property)
symbol_to_id_dict (sfaira.versions.genomes.GenomeContainer property)
symbols (sfaira.versions.genomes.GenomeContainer property)
synonym_node_properties (sfaira.versions.metadata.OntologyCellosaurus property)
(sfaira.versions.metadata.OntologyCl property)
(sfaira.versions.metadata.OntologyHsapdv property)
(sfaira.versions.metadata.OntologyMmusdv property)
(sfaira.versions.metadata.OntologyMondo property)
(sfaira.versions.metadata.OntologyOboCustom property)
(sfaira.versions.metadata.OntologyUberon property)
synonym_node_properties() (sfaira.versions.metadata.OntologyHierarchical method)
(sfaira.versions.metadata.OntologyList method)
(sfaira.versions.metadata.OntologyObo method)
T
tech_sample (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
tech_sample_obs_key (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
title (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
topology_dict (sfaira.train.TrainModelCelltype property)
(sfaira.train.TrainModelEmbedding property)
TopologyContainer (class in sfaira.versions.topologies)
train() (sfaira.estimators.EstimatorKeras method)
(sfaira.estimators.EstimatorKerasCelltype method)
(sfaira.estimators.EstimatorKerasEmbedding method)
train_hyperparam (sfaira.estimators.EstimatorKeras attribute)
TrainModelCelltype (class in sfaira.train)
TrainModelEmbedding (class in sfaira.train)
translate_id_to_symbols() (sfaira.versions.genomes.GenomeContainer method)
translate_symbols_to_id() (sfaira.versions.genomes.GenomeContainer method)
treatment (sfaira.data.DatasetBase attribute)
treatment_obs_key (sfaira.data.DatasetBase attribute)
U
Union (sfaira.train.SummarizeGridsearchEmbedding attribute)
Universe (class in sfaira.data)
UserInterface (class in sfaira.ui)
using_store (sfaira.estimators.EstimatorKerasCelltype property)
(sfaira.estimators.EstimatorKerasEmbedding property)
V
validate_node() (sfaira.versions.metadata.Ontology method)
(sfaira.versions.metadata.OntologyCellosaurus method)
(sfaira.versions.metadata.OntologyCl method)
(sfaira.versions.metadata.OntologyHierarchical method)
(sfaira.versions.metadata.OntologyHsapdv method)
(sfaira.versions.metadata.OntologyList method)
(sfaira.versions.metadata.OntologyMmusdv method)
(sfaira.versions.metadata.OntologyMondo method)
(sfaira.versions.metadata.OntologyObo method)
(sfaira.versions.metadata.OntologyOboCustom method)
(sfaira.versions.metadata.OntologyUberon method)
var (sfaira.data.store.carts.CartMulti property)
(sfaira.data.store.carts.CartSingle attribute)
(sfaira.data.StoreSingleFeatureSpace property)
var_idx (sfaira.data.store.carts.CartSingle attribute)
var_names (sfaira.data.StoreMultipleFeatureSpaceBase property)
(sfaira.data.StoresAnndata property)
(sfaira.data.StoresDao property)
(sfaira.data.StoresH5ad property)
(sfaira.data.StoreSingleFeatureSpace property)
vdj_c_call_obs_key_suffix (sfaira.data.DatasetBase attribute)
vdj_consensus_count_obs_key_suffix (sfaira.data.DatasetBase attribute)
vdj_d_call_obs_key_suffix (sfaira.data.DatasetBase attribute)
vdj_duplicate_count_obs_key_suffix (sfaira.data.DatasetBase attribute)
vdj_j_call_obs_key_suffix (sfaira.data.DatasetBase attribute)
vdj_junction_aa_obs_key_suffix (sfaira.data.DatasetBase attribute)
vdj_junction_obs_key_suffix (sfaira.data.DatasetBase attribute)
vdj_locus_obs_key_suffix (sfaira.data.DatasetBase attribute)
vdj_productive_obs_key_suffix (sfaira.data.DatasetBase attribute)
vdj_v_call_obs_key_suffix (sfaira.data.DatasetBase attribute)
vdj_vdj_1_obs_key_prefix (sfaira.data.DatasetBase attribute)
vdj_vdj_2_obs_key_prefix (sfaira.data.DatasetBase attribute)
vdj_vj_1_obs_key_prefix (sfaira.data.DatasetBase attribute)
vdj_vj_2_obs_key_prefix (sfaira.data.DatasetBase attribute)
version (sfaira.models.celltype.CellTypeMarker property)
(sfaira.models.celltype.CellTypeMlp property)
(sfaira.models.celltype.CellTypeMlpVersioned property)
(sfaira.models.embedding.ModelAeVersioned property)
(sfaira.models.embedding.ModelKerasAe property)
(sfaira.models.embedding.ModelKerasLinear property)
(sfaira.models.embedding.ModelKerasVae property)
(sfaira.models.embedding.ModelKerasVaeIAF property)
(sfaira.models.embedding.ModelKerasVaeVamp property)
(sfaira.models.embedding.ModelLinearVersioned property)
(sfaira.models.embedding.ModelVaeIAFVersioned property)
(sfaira.models.embedding.ModelVaeVampVersioned property)
(sfaira.models.embedding.ModelVaeVersioned property)
W
weights (sfaira.estimators.EstimatorKeras attribute)
write_backed() (sfaira.data.DatasetGroup method)
(sfaira.data.DatasetGroupDirectoryOriented method)
write_best_hyparam() (sfaira.train.GridsearchContainer method)
(sfaira.train.SummarizeGridsearchCelltype method)
(sfaira.train.SummarizeGridsearchEmbedding method)
write_config() (sfaira.data.DatasetSuperGroup method)
(sfaira.data.StoreMultipleFeatureSpaceBase method)
(sfaira.data.StoresAnndata method)
(sfaira.data.StoresDao method)
(sfaira.data.StoresH5ad method)
(sfaira.data.StoreSingleFeatureSpace method)
(sfaira.data.Universe method)
write_distributed_store() (sfaira.data.DatasetBase method)
(sfaira.data.DatasetGroup method)
(sfaira.data.DatasetGroupDirectoryOriented method)
(sfaira.data.DatasetInteractive method)
(sfaira.data.DatasetSuperGroup method)
(sfaira.data.Universe method)
write_lookuptable() (sfaira.ui.UserInterface method)
write_meta() (sfaira.data.DatasetBase method)
(sfaira.data.DatasetInteractive method)
write_ontology_class_maps() (sfaira.data.DatasetBase method)
(sfaira.data.DatasetGroup method)
(sfaira.data.DatasetGroupDirectoryOriented method)
(sfaira.data.DatasetInteractive method)
write_target_universe() (sfaira.versions.metadata.CelltypeUniverse method)
X
x (sfaira.data.store.carts.CartMulti property)
(sfaira.data.store.carts.CartSingle property)
Y
year (sfaira.data.DatasetBase property)
(sfaira.data.DatasetInteractive property)
ytrue() (sfaira.estimators.EstimatorKerasCelltype method)
Z
zoo_celltype (sfaira.ui.UserInterface attribute)
zoo_embedding (sfaira.ui.UserInterface attribute)
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