Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W A abbr (bionty.CellLine attribute) (bionty.CellMarker attribute) (bionty.CellType attribute) (bionty.core.BioRecord attribute) (bionty.DevelopmentalStage attribute) (bionty.Disease attribute) (bionty.Ethnicity attribute) (bionty.ExperimentalFactor attribute) (bionty.Gene attribute) (bionty.models.BioRecord attribute) (bionty.Organism attribute) (bionty.Pathway attribute) (bionty.Phenotype attribute) (bionty.Protein attribute) (bionty.Tissue attribute) (lamindb.Project attribute) (lamindb.Reference attribute) ablocks (lamindb.Artifact attribute) (lamindb.Branch attribute) (lamindb.Collection attribute) (lamindb.Feature attribute) (lamindb.Project attribute) (lamindb.Record attribute) (lamindb.Run attribute) (lamindb.Schema attribute) (lamindb.Space attribute) (lamindb.Transform attribute) (lamindb.ULabel attribute) absolute() (lamindb.UPath method) access_token (lamindb.setup.core.UserSettings attribute) add() (lamindb.models.LabelManager method) (lamindb.models.RelatedManager method) (lamindb.models.SchemaOptionals method) add_column() (lamindb.core.storage.AnnDataAccessor method) add_from() (lamindb.models.LabelManager method) add_new() (lamindb.curators.core.CatVector method) add_new_from() (lamindb.curators.core.DataFrameCatManager method) add_optional_features() (lamindb.Schema method) add_source() (bionty.CellLine class method) (bionty.CellMarker class method) (bionty.CellType class method) (bionty.DevelopmentalStage class method) (bionty.Disease class method) (bionty.Ethnicity class method) (bionty.ExperimentalFactor class method) (bionty.Gene class method) (bionty.models.HasSource class method) (bionty.Organism class method) (bionty.Pathway class method) (bionty.Phenotype class method) (bionty.Protein class method) (bionty.Tissue class method) add_synonym() (bionty.CellLine method) (bionty.CellMarker method) (bionty.CellType method) (bionty.DevelopmentalStage method) (bionty.Disease method) (bionty.Ethnicity method) (bionty.ExperimentalFactor method) (bionty.Gene method) (bionty.Organism method) (bionty.Pathway method) (bionty.Phenotype method) (bionty.Protein method) (bionty.Tissue method) (lamindb.Feature method) (lamindb.models.CanCurate method) (lamindb.Project method) (lamindb.Record method) (lamindb.Reference method) (lamindb.Schema method) (lamindb.ULabel method) (lamindb.User method) add_values() (lamindb.models.FeatureManager method) anchor (lamindb.UPath property) anndata_ensembl_gene_ids_and_valid_features_in_obs() (in module lamindb.examples.schemas) anndata_file_pbmc68k_test() (in module lamindb.examples.datasets) anndata_human_immune_cells() (in module lamindb.examples.datasets) anndata_mouse_sc_lymph_node() (in module lamindb.examples.datasets) anndata_pbmc3k_processed() (in module lamindb.examples.datasets) anndata_pbmc68k_reduced() (in module lamindb.examples.datasets) anndata_suo22_Visium10X() (in module lamindb.examples.datasets) anndata_with_obs() (in module lamindb.examples.datasets) AnnDataAccessor (class in lamindb.core.storage) AnnDataCurator (class in lamindb.curators) annotation (lamindb.core.Settings property) AnnotationSettings (class in lamindb.core.subsettings) api_key (lamindb.setup.core.UserSettings attribute) api_url (lamindb.setup.core.InstanceSettings property) append() (lamindb.Collection method) array_rank (lamindb.Feature attribute) array_shape (lamindb.Feature attribute) array_size (lamindb.Feature attribute) Artifact (class in lamindb) (lamindb.DB attribute) artifact (lamindb.models.ArtifactArtifact attribute) (lamindb.models.ArtifactBlock attribute) (lamindb.models.ArtifactJsonValue attribute) (lamindb.models.ArtifactProject attribute) (lamindb.models.ArtifactRecord attribute) (lamindb.models.ArtifactReference attribute) (lamindb.models.ArtifactRun attribute) (lamindb.models.ArtifactSchema attribute) (lamindb.models.ArtifactULabel attribute) (lamindb.models.ArtifactUser attribute) (lamindb.models.CollectionArtifact attribute) artifact_silence_missing_run_warning (lamindb.core.subsettings.CreationSettings attribute) artifact_skip_size_hash (lamindb.core.subsettings.CreationSettings attribute) ArtifactArtifact (class in lamindb.models) ArtifactBlock (class in lamindb.models) ArtifactJsonValue (class in lamindb.models) ArtifactKind (in module lamindb.base.types) ArtifactProject (class in lamindb.models) ArtifactRecord (class in lamindb.models) ArtifactReference (class in lamindb.models) ArtifactRun (class in lamindb.models) artifacts (bionty.CellLine attribute) (bionty.CellMarker attribute) (bionty.CellType attribute) (bionty.DevelopmentalStage attribute) (bionty.Disease attribute) (bionty.Ethnicity attribute) (bionty.ExperimentalFactor attribute) (bionty.Gene attribute) (bionty.Organism attribute) (bionty.Pathway attribute) (bionty.Phenotype attribute) (bionty.Protein attribute) (bionty.Source attribute) (bionty.Tissue attribute) (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.models.JsonValue attribute) (lamindb.Project attribute) (lamindb.Record attribute) (lamindb.Reference attribute) (lamindb.Run attribute) (lamindb.Schema attribute) (lamindb.Storage attribute) (lamindb.ULabel attribute) (lamindb.User attribute) (pertdb.Biologic attribute) (pertdb.CombinationPerturbation attribute) (pertdb.Compound attribute) (pertdb.CompoundPerturbation attribute) (pertdb.EnvironmentalPerturbation attribute) (pertdb.GeneticPerturbation attribute) (pertdb.PerturbationTarget attribute) ArtifactSchema (class in lamindb.models) ArtifactULabel (class in lamindb.models) ArtifactUser (class in lamindb.models) as_posix() (lamindb.UPath method) as_uri() (lamindb.UPath method) auto_connect (lamindb.setup.core.SetupSettings property) available_spaces (lamindb.setup.core.InstanceSettings property) B BackedAccessor (class in lamindb.core.storage) base26() (in module lamindb.base.uids) base62() (in module lamindb.base.uids) base62_12() (in module lamindb.base.uids) base62_16() (in module lamindb.base.uids) base62_20() (in module lamindb.base.uids) base62_8() (in module lamindb.base.uids) base64() (in module lamindb.base.uids) BaseBlock (class in lamindb.models) BaseSQLRecord (class in lamindb.models) BFXPipeline (class in bionty.base) BigIntegerField (class in lamindb.base.fields) BinaryField (class in lamindb.base.fields) Biologic (class in pertdb) BiologicType (in module pertdb) bionty module bionty (lamindb.DB attribute) bionty.base module bionty.core module bionty.models module bionty.uids module BiontyDB (class in lamindb.models.query_set) BioRecord (class in bionty.core) (class in bionty.models) BioSample (class in bionty.base) biotype (bionty.Gene attribute) BlobHashNotFound Block (class in lamindb.models) block (lamindb.models.BlockProject attribute) BlockProject (class in lamindb.models) blocks (lamindb.Project attribute) BooleanField (class in lamindb.base.fields) branch (bionty.CellLine attribute) (bionty.CellMarker attribute) (bionty.CellType attribute) (bionty.DevelopmentalStage attribute) (bionty.Disease attribute) (bionty.Ethnicity attribute) (bionty.ExperimentalFactor attribute) (bionty.Gene attribute) (bionty.Organism attribute) (bionty.Pathway attribute) (bionty.Phenotype attribute) (bionty.Protein attribute) (bionty.Source attribute) (bionty.Tissue attribute) Branch (class in lamindb) branch (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.core.Context property) Branch (lamindb.DB attribute) branch (lamindb.Feature attribute) (lamindb.models.BranchBlock attribute) (lamindb.models.SQLRecord attribute) (lamindb.Project attribute) (lamindb.Record attribute) (lamindb.Reference attribute) (lamindb.Run attribute) (lamindb.Schema attribute) (lamindb.setup.core.SetupSettings property) (lamindb.Storage attribute) (lamindb.Transform attribute) (lamindb.ULabel attribute) BranchBlock (class in lamindb.models) C cache() (lamindb.Artifact method) (lamindb.Collection method) cache_dir (lamindb.core.Settings property) (lamindb.setup.core.SetupSettings property) (lamindb.setup.core.StorageSettings property) CanCurate (class in lamindb.models) CannotSwitchDefaultInstance canonical_smiles (pertdb.Compound attribute) cat (lamindb.curators.core.ComponentCurator property) (lamindb.curators.DataFrameCurator property) categoricals (lamindb.curators.core.DataFrameCatManager property) CatLookup (class in lamindb.curators.core) CatVector (class in lamindb.curators.core) CellLine (class in bionty) (class in bionty.base) CellMarker (class in bionty) (class in bionty.base) CellType (class in bionty) (class in bionty.base) CharField (class in lamindb.base.fields) check_dtype() (in module lamindb.base.dtypes) check_vars_non_aligned() (lamindb.core.MappedCollection method) check_vars_sorted() (lamindb.core.MappedCollection method) Checkpoint (class in lamindb.integrations.lightning) chembl_id (pertdb.Compound attribute) children (lamindb.Project attribute) (lamindb.Record attribute) (lamindb.ULabel attribute) chmod() (lamindb.UPath method) class_and_instance_method() (in module lamindb.base.utils) clear() (lamindb.models.RelatedManager method) cli_args (lamindb.Run attribute) close() (lamindb.core.MappedCollection method) (lamindb.core.storage.AnnDataAccessor method) closed (lamindb.core.MappedCollection property) (lamindb.core.storage.AnnDataAccessor property) cloud_to_local() (lamindb.setup.core.StorageSettings method) cloud_to_local_no_update() (lamindb.setup.core.StorageSettings method) coerce (lamindb.Feature attribute) (lamindb.Schema attribute) Collection (class in lamindb) (lamindb.DB attribute) collection (lamindb.models.CollectionArtifact attribute) (lamindb.models.CollectionBlock attribute) (lamindb.models.CollectionProject attribute) (lamindb.models.CollectionRecord attribute) (lamindb.models.CollectionReference attribute) (lamindb.models.CollectionULabel attribute) CollectionArtifact (class in lamindb.models) CollectionBlock (class in lamindb.models) CollectionProject (class in lamindb.models) CollectionRecord (class in lamindb.models) CollectionReference (class in lamindb.models) collections (lamindb.Artifact attribute) (lamindb.Project attribute) (lamindb.Record attribute) (lamindb.Reference attribute) (lamindb.ULabel attribute) CollectionULabel (class in lamindb.models) CombinationPerturbation (class in pertdb) component (lamindb.models.SchemaComponent attribute) ComponentCurator (class in lamindb.curators.core) components (lamindb.Schema attribute) composite (lamindb.models.SchemaComponent attribute) composites (lamindb.Schema attribute) Compound (class in pertdb) compound (pertdb.CompoundPerturbation attribute) compound_perturbations (pertdb.CombinationPerturbation attribute) CompoundPerturbation (class in pertdb) concentration (pertdb.CompoundPerturbation attribute) concentration_unit (pertdb.CompoundPerturbation attribute) config (lamindb.models.TransformTransform attribute) connect() (bionty.CellLine class method) (bionty.CellMarker class method) (bionty.CellType class method) (bionty.DevelopmentalStage class method) (bionty.Disease class method) (bionty.Ethnicity class method) (bionty.ExperimentalFactor class method) (bionty.Gene class method) (bionty.Organism class method) (bionty.Pathway class method) (bionty.Phenotype class method) (bionty.Protein class method) (bionty.Source class method) (bionty.Tissue class method) (in module lamindb) (lamindb.Artifact class method) (lamindb.Branch class method) (lamindb.Collection class method) (lamindb.Feature class method) (lamindb.models.BaseSQLRecord class method) (lamindb.Project class method) (lamindb.Record class method) (lamindb.Reference class method) (lamindb.Run class method) (lamindb.Schema class method) (lamindb.Space class method) (lamindb.Storage class method) (lamindb.Transform class method) (lamindb.ULabel class method) (lamindb.User class method) Context (class in lamindb.core) context (in module lamindb) create() (lamindb.setup.migrate class method) create_cellxgene_schema() (in module lamindb.examples.cellxgene) created_artifacts (lamindb.User attribute) created_at (bionty.CellLine attribute) (bionty.CellMarker attribute) (bionty.CellType attribute) (bionty.DevelopmentalStage attribute) (bionty.Disease attribute) (bionty.Ethnicity attribute) (bionty.ExperimentalFactor attribute) (bionty.Gene attribute) (bionty.Organism attribute) (bionty.Pathway attribute) (bionty.Phenotype attribute) (bionty.Protein attribute) (bionty.Source attribute) (bionty.Tissue attribute) (lamindb.Artifact attribute) (lamindb.Branch attribute) (lamindb.Collection attribute) (lamindb.Feature attribute) (lamindb.models.RunJsonValue attribute) (lamindb.models.RunProject attribute) (lamindb.models.RunRecord attribute) (lamindb.models.RunULabel attribute) (lamindb.models.TransformTransform attribute) (lamindb.Project attribute) (lamindb.Record attribute) (lamindb.Reference attribute) (lamindb.Run attribute) (lamindb.Schema attribute) (lamindb.Space attribute) (lamindb.Storage attribute) (lamindb.Transform attribute) (lamindb.ULabel attribute) (lamindb.User attribute) created_by (bionty.CellLine attribute) (bionty.CellMarker attribute) (bionty.CellType attribute) (bionty.DevelopmentalStage attribute) (bionty.Disease attribute) (bionty.Ethnicity attribute) (bionty.ExperimentalFactor attribute) (bionty.Gene attribute) (bionty.Organism attribute) (bionty.Pathway attribute) (bionty.Phenotype attribute) (bionty.Protein attribute) (bionty.Source attribute) (bionty.Tissue attribute) (lamindb.Artifact attribute) (lamindb.Branch attribute) (lamindb.Collection attribute) (lamindb.Feature attribute) (lamindb.models.BaseBlock attribute) (lamindb.models.RunJsonValue attribute) (lamindb.models.RunProject attribute) (lamindb.models.RunRecord attribute) (lamindb.models.RunULabel attribute) (lamindb.models.TracksRun attribute) (lamindb.models.TransformTransform attribute) (lamindb.Project attribute) (lamindb.Record attribute) (lamindb.Reference attribute) (lamindb.Run attribute) (lamindb.Schema attribute) (lamindb.Space attribute) (lamindb.Storage attribute) (lamindb.Transform attribute) (lamindb.ULabel attribute) created_by_id (lamindb.models.BaseBlock attribute) (lamindb.models.TracksRun attribute) created_runs (lamindb.User attribute) created_transforms (lamindb.User attribute) creation (lamindb.core.Settings property) CreationSettings (class in lamindb.core.subsettings) curate_from_croissant() (in module lamindb.integrations) Curator (class in lamindb.curators.core) CurrentInstanceNotConfigured currently_used (bionty.Source attribute) cwd() (lamindb.UPath class method) D data_artifact (lamindb.Collection property) dataframe_artifact (bionty.Source attribute) DataFrameCatManager (class in lamindb.curators.core) DataFrameCurator (class in lamindb.curators) date (lamindb.Reference attribute) DateField (class in lamindb.base.fields) DateTimeField (class in lamindb.base.fields) DB (class in lamindb) db (lamindb.setup.core.InstanceSettings property) DecimalField (class in lamindb.base.fields) default_value (lamindb.Feature attribute) define_features_labels() (in module lamindb.examples.datasets.mini_immuno) define_mini_immuno_schema_flexible() (in module lamindb.examples.datasets.mini_immuno) defined_migrations() (lamindb.setup.migrate class method) delete() (bionty.CellLine method) (bionty.CellMarker method) (bionty.CellType method) (bionty.DevelopmentalStage method) (bionty.Disease method) (bionty.Ethnicity method) (bionty.ExperimentalFactor method) (bionty.Gene method) (bionty.Organism method) (bionty.Pathway method) (bionty.Phenotype method) (bionty.Protein method) (bionty.Source method) (bionty.Tissue method) (in module lamindb.setup) (lamindb.Artifact method) (lamindb.Branch method) (lamindb.Collection method) (lamindb.Feature method) (lamindb.models.BaseSQLRecord method) (lamindb.models.SQLRecord method) (lamindb.Project method) (lamindb.Record method) (lamindb.Reference method) (lamindb.Run method) (lamindb.Schema method) (lamindb.Space method) (lamindb.Storage method) (lamindb.Transform method) (lamindb.ULabel method) (lamindb.User method) deploy() (lamindb.setup.migrate class method) deployed_migrations() (lamindb.setup.migrate class method) deprecated() (in module lamindb.base.utils) describe() (bionty.CellLine class method) (bionty.CellMarker class method) (bionty.CellType class method) (bionty.DevelopmentalStage class method) (bionty.Disease class method) (bionty.Ethnicity class method) (bionty.ExperimentalFactor class method) (bionty.Gene class method) (bionty.Organism class method) (bionty.Pathway class method) (bionty.Phenotype class method) (bionty.Protein class method) (bionty.Source class method) (bionty.Tissue class method) (lamindb.Artifact class method) (lamindb.Branch class method) (lamindb.Collection class method) (lamindb.Feature class method) (lamindb.models.BaseSQLRecord method) (lamindb.models.FeatureManager method) (lamindb.models.LabelManager method) (lamindb.Project class method) (lamindb.Record class method) (lamindb.Reference class method) (lamindb.Run class method) (lamindb.Schema method) (lamindb.Space class method) (lamindb.Storage class method) (lamindb.Transform class method) (lamindb.ULabel class method) (lamindb.User class method) description (bionty.CellLine attribute) (bionty.CellMarker attribute) (bionty.CellType attribute) (bionty.core.BioRecord attribute) (bionty.DevelopmentalStage attribute) (bionty.Disease attribute) (bionty.Ethnicity attribute) (bionty.ExperimentalFactor attribute) (bionty.Gene attribute) (bionty.models.BioRecord attribute) (bionty.Organism attribute) (bionty.Pathway attribute) (bionty.Phenotype attribute) (bionty.Protein attribute) (bionty.Source attribute) (bionty.Tissue attribute) (lamindb.Artifact attribute) (lamindb.Branch attribute) (lamindb.Collection attribute) (lamindb.core.Context property) (lamindb.Feature attribute) (lamindb.Project attribute) (lamindb.Record attribute) (lamindb.Reference attribute) (lamindb.Schema attribute) (lamindb.Space attribute) (lamindb.Storage attribute) (lamindb.Transform attribute) (lamindb.ULabel attribute) dev_dir (lamindb.setup.core.SetupSettings property) DevelopmentalStage (class in bionty) (class in bionty.base) df (lamindb.models.InspectResult property) df_iris() (in module lamindb.examples.datasets) df_iris_in_meter() (in module lamindb.examples.datasets) df_iris_in_meter_study1() (in module lamindb.examples.datasets) df_iris_in_meter_study2() (in module lamindb.examples.datasets) dialect (lamindb.setup.core.InstanceSettings property) dict_cellxgene_uns() (in module lamindb.examples.datasets) dir_iris_images() (in module lamindb.examples.datasets) dir_scrnaseq_cellranger() (in module lamindb.examples.datasets) disconnect() (in module lamindb.setup) Disease (class in bionty) (class in bionty.base) display_currently_used_sources() (in module bionty.base) display_sources() (in module bionty.base) django() (in module lamindb.setup) doc_args() (in module lamindb.base.utils) doi (lamindb.Reference attribute) download_to() (lamindb.UPath method) drive (lamindb.UPath property) Drug (class in bionty.base) dtype (lamindb.Schema property) dtype_as_object (lamindb.Feature property) dtype_as_str (lamindb.Feature property) DtypeStr (in module lamindb.base.types) duration (pertdb.CompoundPerturbation attribute) (pertdb.EnvironmentalPerturbation attribute) DurationField (class in lamindb.base.fields) E email (lamindb.setup.core.UserSettings attribute) EmailField (class in lamindb.base.fields) end_date (lamindb.Project attribute) ensembl_gene_id (bionty.Gene attribute) ensembl_gene_ids (bionty.Protein attribute) entity (bionty.Source attribute) entrypoint (lamindb.Run attribute) environment (lamindb.Run attribute) (lamindb.Transform attribute) environmental_perturbations (pertdb.CombinationPerturbation attribute) EnvironmentalPerturbation (class in pertdb) Ethnicity (class in bionty) (class in bionty.base) exists() (lamindb.UPath method) expanduser() (lamindb.UPath method) ExperimentalFactor (class in bionty) (class in bionty.base) extra_data (lamindb.Record attribute) F fake_bio_notebook_titles() (in module lamindb.examples.datasets) Feature (class in lamindb) (lamindb.DB attribute) feature (lamindb.models.ArtifactArtifact attribute) (lamindb.models.ArtifactProject attribute) (lamindb.models.ArtifactRecord attribute) (lamindb.models.ArtifactReference attribute) (lamindb.models.ArtifactRun attribute) (lamindb.models.ArtifactULabel attribute) (lamindb.models.ArtifactUser attribute) (lamindb.models.CollectionRecord attribute) (lamindb.models.CollectionULabel attribute) (lamindb.models.FeatureBlock attribute) (lamindb.models.FeatureProject attribute) (lamindb.models.JsonValue attribute) (lamindb.models.ProjectRecord attribute) (lamindb.models.RecordArtifact attribute) (lamindb.models.RecordCollection attribute) (lamindb.models.RecordJson attribute) (lamindb.models.RecordProject attribute) (lamindb.models.RecordRecord attribute) (lamindb.models.RecordReference attribute) (lamindb.models.RecordRun attribute) (lamindb.models.RecordTransform attribute) (lamindb.models.RecordULabel attribute) (lamindb.models.RecordUser attribute) (lamindb.models.ReferenceRecord attribute) (lamindb.models.RunRecord attribute) (lamindb.models.SchemaFeature attribute) (lamindb.models.TransformRecord attribute) feature_ref_is_semantic (lamindb.models.ArtifactSchema attribute) FeatureBlock (class in lamindb.models) FeatureManager (class in lamindb.models) FeatureProject (class in lamindb.models) features (lamindb.Artifact property) (lamindb.Feature attribute) (lamindb.Project attribute) (lamindb.Record property) (lamindb.Run property) (lamindb.Schema attribute) FieldAttr (in module lamindb.base.types) FieldValidationError file_bam() (in module lamindb.examples.datasets) file_fastq() (in module lamindb.examples.datasets) file_fcs() (in module lamindb.examples.datasets) file_fcs_alpert19() (in module lamindb.examples.datasets) file_jpg_paradisi05() (in module lamindb.examples.datasets) file_mini_csv() (in module lamindb.examples.datasets) file_tiff_suo22() (in module lamindb.examples.datasets) file_tsv_rnaseq_nfcore_salmon_merged_gene_counts() (in module lamindb.examples.datasets) FileNotInDevDir filter() (bionty.CellLine class method) (bionty.CellMarker class method) (bionty.CellType class method) (bionty.DevelopmentalStage class method) (bionty.Disease class method) (bionty.Ethnicity class method) (bionty.ExperimentalFactor class method) (bionty.Gene class method) (bionty.Organism class method) (bionty.Pathway class method) (bionty.Phenotype class method) (bionty.Protein class method) (bionty.Source class method) (bionty.Tissue class method) (lamindb.Artifact method) (lamindb.Branch class method) (lamindb.Collection class method) (lamindb.Feature class method) (lamindb.models.BaseSQLRecord class method) (lamindb.models.QuerySet method) (lamindb.Project class method) (lamindb.Record class method) (lamindb.Reference class method) (lamindb.Run method) (lamindb.Schema class method) (lamindb.Space class method) (lamindb.Storage class method) (lamindb.Transform class method) (lamindb.ULabel class method) (lamindb.User class method) finish() (in module lamindb) finished_at (lamindb.Run attribute) flexible (lamindb.Schema attribute) FloatField (class in lamindb.base.fields) flow() (in module lamindb) ForeignKey (class in lamindb.base.fields) frac_validated (lamindb.models.InspectResult property) from_anndata() (lamindb.Artifact class method) from_dataframe() (lamindb.Artifact class method) (lamindb.Feature class method) (lamindb.Schema class method) from_dict() (lamindb.Feature class method) from_dir() (lamindb.Artifact class method) from_git() (lamindb.Transform class method) from_lazy() (lamindb.Artifact class method) from_mudata() (lamindb.Artifact class method) from_source() (bionty.CellLine class method) (bionty.CellMarker class method) (bionty.CellType class method) (bionty.DevelopmentalStage class method) (bionty.Disease class method) (bionty.Ethnicity class method) (bionty.ExperimentalFactor class method) (bionty.Gene class method) (bionty.models.HasSource class method) (bionty.Organism class method) (bionty.Pathway class method) (bionty.Phenotype class method) (bionty.Protein class method) (bionty.Tissue class method) from_spatialdata() (lamindb.Artifact class method) from_tiledbsoma() (lamindb.Artifact class method) from_values() (bionty.CellLine class method) (bionty.CellMarker class method) (bionty.CellType class method) (bionty.DevelopmentalStage class method) (bionty.Disease class method) (bionty.Ethnicity class method) (bionty.ExperimentalFactor class method) (bionty.Gene class method) (bionty.Organism class method) (bionty.Pathway class method) (bionty.Phenotype class method) (bionty.Protein class method) (bionty.Tissue class method) (lamindb.Feature class method) (lamindb.models.CanCurate method) (lamindb.Project class method) (lamindb.Record class method) (lamindb.Reference class method) (lamindb.Schema class method) (lamindb.ULabel class method) (lamindb.User class method) fs (lamindb.UPath property) G Gene (class in bionty) (class in bionty.base) gene_symbol (bionty.CellMarker attribute) (bionty.Protein attribute) GenericIPAddressField (class in lamindb.base.fields) genes (bionty.Pathway attribute) (pertdb.PerturbationTarget attribute) genetic_perturbations (pertdb.CombinationPerturbation attribute) GeneticPerturbation (class in pertdb) GeneticPerturbationSystem (in module pertdb) get() (bionty.CellLine class method) (bionty.CellMarker class method) (bionty.CellType class method) (bionty.DevelopmentalStage class method) (bionty.Disease class method) (bionty.Ethnicity class method) (bionty.ExperimentalFactor class method) (bionty.Gene class method) (bionty.Organism class method) (bionty.Pathway class method) (bionty.Phenotype class method) (bionty.Protein class method) (bionty.Source class method) (bionty.Tissue class method) (lamindb.Artifact method) (lamindb.Branch class method) (lamindb.Collection method) (lamindb.Feature class method) (lamindb.models.BaseSQLRecord class method) (lamindb.models.LabelManager method) (lamindb.models.QuerySet method) (lamindb.models.SchemaOptionals method) (lamindb.Project class method) (lamindb.Record class method) (lamindb.Reference class method) (lamindb.Run class method) (lamindb.Schema class method) (lamindb.Space class method) (lamindb.Storage class method) (lamindb.Transform class method) (lamindb.ULabel class method) (lamindb.User class method) get_dataset1() (in module lamindb.examples.datasets.mini_immuno) get_dataset2() (in module lamindb.examples.datasets.mini_immuno) get_label_weights() (lamindb.core.MappedCollection method) get_merged_categories() (lamindb.core.MappedCollection method) get_merged_labels() (lamindb.core.MappedCollection method) get_or_create() (lamindb.models.JsonValue class method) get_queryset() (lamindb.models.QueryManager method) get_uids() (lamindb.models.SchemaOptionals method) get_values() (lamindb.models.FeatureManager method) git_repo (lamindb.setup.core.InstanceSettings property) glob() (lamindb.UPath method) group() (lamindb.UPath method) H handle (lamindb.setup.core.UserSettings attribute) (lamindb.User attribute) hardlink_to() (lamindb.UPath method) hash (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.models.JsonValue attribute) (lamindb.Schema attribute) (lamindb.Transform attribute) HasOntologyId (class in bionty.models) HasParents (class in lamindb.models) HasSource (class in bionty.models) HasType (class in lamindb.models) home() (lamindb.UPath class method) host (lamindb.setup.core.StorageSettings property) (lamindb.Storage property) I id (lamindb.setup.core.UserSettings property) import_source() (bionty.CellLine class method) (bionty.CellMarker class method) (bionty.CellType class method) (bionty.DevelopmentalStage class method) (bionty.Disease class method) (bionty.Ethnicity class method) (bionty.ExperimentalFactor class method) (bionty.Gene class method) (bionty.models.HasSource class method) (bionty.Organism class method) (bionty.Pathway class method) (bionty.Phenotype class method) (bionty.Protein class method) (bionty.Tissue class method) in_db (bionty.Source attribute) inchikey (pertdb.Compound attribute) index (lamindb.Schema property) init() (in module lamindb.setup) initiated_by_run (lamindb.Run attribute) initiated_runs (lamindb.Run attribute) input_artifacts (lamindb.Run attribute) input_collections (lamindb.Run attribute) input_of_runs (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.Record attribute) input_records (lamindb.Run attribute) inspect() (bionty.CellLine class method) (bionty.CellMarker class method) (bionty.CellType class method) (bionty.DevelopmentalStage class method) (bionty.Disease class method) (bionty.Ethnicity class method) (bionty.ExperimentalFactor class method) (bionty.Gene class method) (bionty.Organism class method) (bionty.Pathway class method) (bionty.Phenotype class method) (bionty.Protein class method) (bionty.Tissue class method) (lamindb.Feature class method) (lamindb.models.CanCurate method) (lamindb.Project class method) (lamindb.Record class method) (lamindb.Reference class method) (lamindb.Schema class method) (lamindb.ULabel class method) (lamindb.User class method) InspectResult (class in lamindb.models) instance (lamindb.setup.core.SetupSettings property) instance_uid (lamindb.core.Settings property) (lamindb.setup.core.StorageSettings property) (lamindb.Storage attribute) InstanceLockedException InstanceNotCreated InstanceNotFoundError InstanceSettings (class in lamindb.setup.core) IntegerField (class in lamindb.base.fields) IntegrityError InvalidArgument is_absolute() (lamindb.UPath method) is_block_device() (lamindb.UPath method) is_char_device() (lamindb.UPath method) is_connected (lamindb.setup.core.SetupSettings property) is_dir() (lamindb.UPath method) is_fifo() (lamindb.UPath method) is_file() (lamindb.UPath method) is_junction() (lamindb.UPath method) is_latest (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.Transform attribute) is_locked (bionty.CellLine attribute) (bionty.CellMarker attribute) (bionty.CellType attribute) (bionty.DevelopmentalStage attribute) (bionty.Disease attribute) (bionty.Ethnicity attribute) (bionty.ExperimentalFactor attribute) (bionty.Gene attribute) (bionty.Organism attribute) (bionty.Pathway attribute) (bionty.Phenotype attribute) (bionty.Protein attribute) (bionty.Source attribute) (bionty.Tissue attribute) (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.Feature attribute) (lamindb.models.SQLRecord attribute) (lamindb.Project attribute) (lamindb.Record attribute) (lamindb.Reference attribute) (lamindb.Run attribute) (lamindb.Schema attribute) (lamindb.Storage attribute) (lamindb.Transform attribute) (lamindb.ULabel attribute) is_managed_by_hub (lamindb.setup.core.InstanceSettings property) is_mount() (lamindb.UPath method) is_on_hub (lamindb.setup.core.InstanceSettings property) (lamindb.setup.core.StorageSettings property) is_read_only_connection (lamindb.setup.core.InstanceSettings property) is_relative_to() (lamindb.UPath method) is_remote (lamindb.setup.core.InstanceSettings property) is_reserved() (lamindb.UPath method) is_sheet (lamindb.Record property) is_socket() (lamindb.UPath method) is_symlink() (lamindb.UPath method) is_type (lamindb.Feature attribute) (lamindb.Project attribute) (lamindb.Record attribute) (lamindb.Reference attribute) (lamindb.Schema attribute) (lamindb.ULabel attribute) is_validated (lamindb.curators.core.CatVector property) IsVersioned (class in lamindb.models) iterdir() (lamindb.UPath method) itype (lamindb.Schema attribute) J joinpath() (lamindb.UPath method) joinuri() (lamindb.UPath method) json_values (lamindb.Artifact attribute) (lamindb.Run attribute) JSONField (class in lamindb.base.fields) JsonValue (class in lamindb.models) jsonvalue (lamindb.models.ArtifactJsonValue attribute) (lamindb.models.RunJsonValue attribute) K keep_artifacts_local (lamindb.setup.core.InstanceSettings property) key (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.models.Block attribute) (lamindb.Transform attribute) key_to_filepath() (lamindb.setup.core.StorageSettings method) kind (lamindb.Artifact attribute) (lamindb.Transform attribute) L LabelManager (class in lamindb.models) labels (lamindb.Artifact property) lamindb module lamindb.base module lamindb.base.dtypes module lamindb.base.fields module lamindb.base.types module lamindb.base.uids module lamindb.base.utils module lamindb.core module lamindb.core.loaders module lamindb.core.storage module lamindb.core.subsettings module lamindb.curators module lamindb.curators.core module lamindb.errors module lamindb.examples module lamindb.examples.cellxgene module lamindb.examples.croissant module lamindb.examples.datasets module lamindb.examples.datasets.mini_immuno module lamindb.examples.mlflow module lamindb.examples.schemas module lamindb.examples.wandb module lamindb.integrations module lamindb.integrations.lightning module lamindb.models module lamindb.setup module lamindb.setup.core module lamindb.setup.errors module lamindb.setup.types module latest_run (lamindb.Transform property) LazyArtifact (class in lamindb.models) lchmod() (lamindb.UPath method) length (bionty.Protein attribute) line_number (lamindb.models.TransformBlock attribute) linked_artifacts (lamindb.Record attribute) linked_by_artifacts (lamindb.Artifact attribute) linked_collections (lamindb.Record attribute) linked_in_records (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.Project attribute) (lamindb.Record attribute) (lamindb.Reference attribute) (lamindb.Run attribute) (lamindb.Transform attribute) (lamindb.ULabel attribute) (lamindb.User attribute) linked_projects (lamindb.Record attribute) linked_records (lamindb.Record attribute) linked_references (lamindb.Record attribute) linked_runs (lamindb.Record attribute) linked_transforms (lamindb.Record attribute) linked_ulabels (lamindb.Record attribute) linked_users (lamindb.Record attribute) ListLike (in module lamindb.base.types) load() (lamindb.Artifact method) (lamindb.Collection method) load_fcs() (in module lamindb.core.loaders) load_h5ad() (in module lamindb.core.loaders) load_h5mu() (in module lamindb.core.loaders) load_html() (in module lamindb.core.loaders) load_image() (in module lamindb.core.loaders) load_json() (in module lamindb.core.loaders) load_svg() (in module lamindb.core.loaders) load_tsv() (in module lamindb.core.loaders) local_filepath() (lamindb.setup.core.StorageSettings method) local_storage (lamindb.core.Settings property) (lamindb.setup.core.InstanceSettings property) logger (in module lamindb.core) login() (in module lamindb.setup) logout() (in module lamindb.setup) lookup() (bionty.CellLine class method) (bionty.CellMarker class method) (bionty.CellType class method) (bionty.DevelopmentalStage class method) (bionty.Disease class method) (bionty.Ethnicity class method) (bionty.ExperimentalFactor class method) (bionty.Gene class method) (bionty.Organism class method) (bionty.Pathway class method) (bionty.Phenotype class method) (bionty.Protein class method) (bionty.Source class method) (bionty.Tissue class method) (lamindb.Artifact class method) (lamindb.Branch class method) (lamindb.Collection class method) (lamindb.curators.core.DataFrameCatManager method) (lamindb.Feature class method) (lamindb.models.BaseSQLRecord class method) (lamindb.models.QueryManager method) (lamindb.Project class method) (lamindb.Record class method) (lamindb.Reference class method) (lamindb.Run class method) (lamindb.Schema class method) (lamindb.Space class method) (lamindb.Storage class method) (lamindb.Transform class method) (lamindb.ULabel class method) (lamindb.User class method) lstat() (lamindb.UPath method) M mapped() (lamindb.Collection method) MappedCollection (class in lamindb.core) match() (lamindb.UPath method) maximal_set (lamindb.Schema attribute) md5 (bionty.Source attribute) members (lamindb.Schema property) (pertdb.CombinationPerturbation property) meta_artifact (lamindb.Collection attribute) migrate (class in lamindb.setup) mini_immuno() (in module lamindb.examples.croissant) minimal_set (lamindb.Schema attribute) MissingContextUID mkdir() (lamindb.UPath method) moa (pertdb.Compound attribute) modified (lamindb.UPath property) module bionty bionty.base bionty.core bionty.models bionty.uids lamindb lamindb.base lamindb.base.dtypes lamindb.base.fields lamindb.base.types lamindb.base.uids lamindb.base.utils lamindb.core lamindb.core.loaders lamindb.core.storage lamindb.core.subsettings lamindb.curators lamindb.curators.core lamindb.errors lamindb.examples lamindb.examples.cellxgene lamindb.examples.croissant lamindb.examples.datasets lamindb.examples.datasets.mini_immuno lamindb.examples.mlflow lamindb.examples.schemas lamindb.examples.wandb lamindb.integrations lamindb.integrations.lightning lamindb.models lamindb.setup lamindb.setup.core lamindb.setup.errors lamindb.setup.types pertdb modules (lamindb.setup.core.InstanceSettings property) ModuleWasntConfigured molformula (pertdb.Compound attribute) molweight (pertdb.Compound attribute) mudata_papalexi21_subset() (in module lamindb.examples.datasets) MuDataCurator (class in lamindb.curators) MultipleObjectsReturned N n_empty (lamindb.models.InspectResult property) n_files (lamindb.Artifact attribute) n_max_records (lamindb.core.subsettings.AnnotationSettings attribute) n_members (lamindb.Schema attribute) n_observations (lamindb.Artifact attribute) n_unique (lamindb.models.InspectResult property) name (bionty.CellLine attribute) (bionty.CellMarker attribute) (bionty.CellType attribute) (bionty.DevelopmentalStage attribute) (bionty.Disease attribute) (bionty.Ethnicity attribute) (bionty.ExperimentalFactor attribute) (bionty.Organism attribute) (bionty.Pathway attribute) (bionty.Phenotype attribute) (bionty.Protein attribute) (bionty.Source attribute) (bionty.Tissue attribute) (lamindb.Branch attribute) (lamindb.Collection property) (lamindb.Feature attribute) (lamindb.Project attribute) (lamindb.Record attribute) (lamindb.Reference attribute) (lamindb.Run attribute) (lamindb.Schema attribute) (lamindb.setup.core.InstanceSettings property) (lamindb.setup.core.UserSettings attribute) (lamindb.Space attribute) (lamindb.ULabel attribute) (lamindb.UPath property) (lamindb.User attribute) (pertdb.Biologic attribute) (pertdb.CombinationPerturbation attribute) (pertdb.CompoundPerturbation attribute) (pertdb.EnvironmentalPerturbation attribute) (pertdb.GeneticPerturbation attribute) (pertdb.PerturbationTarget attribute) ncbi_gene_id (bionty.CellMarker attribute) ncbi_gene_ids (bionty.Gene attribute) non_validated (lamindb.curators.core.DataFrameCatManager property) (lamindb.models.InspectResult property) NotebookNotSaved NoWriteAccess nullable (lamindb.Feature attribute) O ObjectDoesNotExist off_target_score (pertdb.GeneticPerturbation attribute) on_target_score (pertdb.GeneticPerturbation attribute) OneToOneField (class in lamindb.base.fields) ontology() (in module bionty.uids) ontology_id (bionty.CellLine attribute) (bionty.CellType attribute) (bionty.DevelopmentalStage attribute) (bionty.Disease attribute) (bionty.Ethnicity attribute) (bionty.ExperimentalFactor attribute) (bionty.Organism attribute) (bionty.Pathway attribute) (bionty.Phenotype attribute) (bionty.Tissue attribute) (pertdb.EnvironmentalPerturbation attribute) open() (lamindb.Artifact method) (lamindb.Collection method) (lamindb.UPath method) optionals (lamindb.Schema property) ordered_artifacts (lamindb.Collection property) ordered_set (lamindb.Schema attribute) organism (bionty.CellMarker attribute) (bionty.core.Settings property) (bionty.Gene attribute) (bionty.Protein attribute) (bionty.Source attribute) Organism (class in bionty) (class in bionty.base) original_shapes (lamindb.core.MappedCollection property) otype (lamindb.Artifact attribute) (lamindb.Schema attribute) output_artifacts (lamindb.Run attribute) output_collections (lamindb.Run attribute) output_records (lamindb.Run attribute) overwrite_versions (lamindb.Artifact property) owner (lamindb.setup.core.InstanceSettings property) owner() (lamindb.UPath method) P params (lamindb.Run attribute) parent (lamindb.UPath property) parents (bionty.CellLine attribute) (bionty.CellType attribute) (bionty.DevelopmentalStage attribute) (bionty.Disease attribute) (bionty.Ethnicity attribute) (bionty.ExperimentalFactor attribute) (bionty.models.HasOntologyId attribute) (bionty.Organism attribute) (bionty.Pathway attribute) (bionty.Phenotype attribute) (bionty.Tissue attribute) (lamindb.Project attribute) (lamindb.Record attribute) (lamindb.ULabel attribute) (lamindb.UPath property) parts (lamindb.UPath property) password (lamindb.setup.core.UserSettings attribute) path (lamindb.Artifact property) (lamindb.models.LazyArtifact property) (lamindb.Storage property) (lamindb.UPath property) paths (lamindb.setup.core.SetupSettings property) Pathway (class in bionty) (class in bionty.base) pathways (pertdb.PerturbationTarget attribute) pertdb module pertdb (lamindb.DB attribute) PertdbDB (class in lamindb.models.query_set) PerturbationTarget (class in pertdb) Phenotype (class in bionty) (class in bionty.base) PositiveIntegerField (class in lamindb.base.fields) PositiveSmallIntegerField (class in lamindb.base.fields) predecessor (lamindb.models.TransformTransform attribute) predecessors (lamindb.Project attribute) (lamindb.Transform attribute) private_django_api (lamindb.setup.core.SetupSettings property) Project (class in lamindb) project (lamindb.core.Context property) Project (lamindb.DB attribute) project (lamindb.models.ArtifactProject attribute) (lamindb.models.BlockProject attribute) (lamindb.models.CollectionProject attribute) (lamindb.models.FeatureProject attribute) (lamindb.models.ProjectBlock attribute) (lamindb.models.ProjectRecord attribute) (lamindb.models.RunProject attribute) (lamindb.models.SchemaProject attribute) (lamindb.models.TransformProject attribute) (lamindb.models.ULabelProject attribute) ProjectBlock (class in lamindb.models) ProjectRecord (class in lamindb.models) projects (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.Feature attribute) (lamindb.models.Block attribute) (lamindb.Project attribute) (lamindb.Record attribute) (lamindb.Reference attribute) (lamindb.Run attribute) (lamindb.Schema attribute) (lamindb.Transform attribute) (lamindb.ULabel attribute) Protein (class in bionty) (class in bionty.base) proteins (pertdb.Biologic attribute) (pertdb.PerturbationTarget attribute) protocol (lamindb.UPath property) public() (bionty.CellLine class method) (bionty.CellMarker class method) (bionty.CellType class method) (bionty.DevelopmentalStage class method) (bionty.Disease class method) (bionty.Ethnicity class method) (bionty.ExperimentalFactor class method) (bionty.Gene class method) (bionty.models.HasSource class method) (bionty.Organism class method) (bionty.Pathway class method) (bionty.Phenotype class method) (bionty.Protein class method) (bionty.Tissue class method) PublicOntology (class in bionty.base) PublicOntologyField (class in bionty.base) pubmed_id (lamindb.Reference attribute) Q query_children() (bionty.CellLine method) (bionty.CellType method) (bionty.DevelopmentalStage method) (bionty.Disease method) (bionty.Ethnicity method) (bionty.ExperimentalFactor method) (bionty.Organism method) (bionty.Pathway method) (bionty.Phenotype method) (bionty.Tissue method) (lamindb.models.HasParents method) (lamindb.Record method) (lamindb.ULabel method) query_features() (lamindb.Feature method) query_parents() (bionty.CellLine method) (bionty.CellType method) (bionty.DevelopmentalStage method) (bionty.Disease method) (bionty.Ethnicity method) (bionty.ExperimentalFactor method) (bionty.Organism method) (bionty.Pathway method) (bionty.Phenotype method) (bionty.Tissue method) (lamindb.models.HasParents method) (lamindb.Record method) (lamindb.ULabel method) query_projects() (lamindb.Project method) query_records() (lamindb.Record method) query_references() (lamindb.Reference method) query_schemas() (lamindb.Schema method) query_types() (lamindb.Feature method) (lamindb.models.HasType method) (lamindb.Project method) (lamindb.Record method) (lamindb.Reference method) (lamindb.Schema method) (lamindb.ULabel method) query_ulabels() (lamindb.ULabel method) QueryManager (class in lamindb.models) QuerySet (class in lamindb.models) R read_bytes() (lamindb.UPath method) read_text() (lamindb.UPath method) readlink() (lamindb.UPath method) Record (class in lamindb) (lamindb.DB attribute) record (lamindb.models.ArtifactRecord attribute) (lamindb.models.CollectionRecord attribute) (lamindb.models.ProjectRecord attribute) (lamindb.models.RecordArtifact attribute) (lamindb.models.RecordBlock attribute) (lamindb.models.RecordCollection attribute) (lamindb.models.RecordJson attribute) (lamindb.models.RecordProject attribute) (lamindb.models.RecordRecord attribute) (lamindb.models.RecordReference attribute) (lamindb.models.RecordRun attribute) (lamindb.models.RecordTransform attribute) (lamindb.models.RecordULabel attribute) (lamindb.models.RecordUser attribute) (lamindb.models.ReferenceRecord attribute) (lamindb.models.RunRecord attribute) (lamindb.models.TransformRecord attribute) (lamindb.setup.core.StorageSettings property) RecordArtifact (class in lamindb.models) RecordBlock (class in lamindb.models) RecordCollection (class in lamindb.models) RecordJson (class in lamindb.models) RecordProject (class in lamindb.models) RecordRecord (class in lamindb.models) RecordReference (class in lamindb.models) RecordRun (class in lamindb.models) records (bionty.CellLine attribute) (bionty.CellMarker attribute) (bionty.CellType attribute) (bionty.DevelopmentalStage attribute) (bionty.Disease attribute) (bionty.Ethnicity attribute) (bionty.ExperimentalFactor attribute) (bionty.Gene attribute) (bionty.Organism attribute) (bionty.Pathway attribute) (bionty.Phenotype attribute) (bionty.Protein attribute) (bionty.Tissue attribute) (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.Project attribute) (lamindb.Record attribute) (lamindb.Reference attribute) (lamindb.Run attribute) (lamindb.Schema attribute) (lamindb.Transform attribute) RecordTransform (class in lamindb.models) RecordULabel (class in lamindb.models) RecordUser (class in lamindb.models) recreated_artifacts (lamindb.Run attribute) recreated_collections (lamindb.Run attribute) recreating_runs (lamindb.Artifact attribute) (lamindb.Collection attribute) Reference (class in lamindb) reference (lamindb.Collection attribute) Reference (lamindb.DB attribute) reference (lamindb.models.ArtifactReference attribute) (lamindb.models.CollectionReference attribute) (lamindb.models.ReferenceRecord attribute) (lamindb.models.TransformReference attribute) (lamindb.Record attribute) (lamindb.Run attribute) (lamindb.Transform attribute) (lamindb.ULabel attribute) reference_type (lamindb.Collection attribute) (lamindb.Record attribute) (lamindb.Run attribute) (lamindb.Transform attribute) (lamindb.ULabel attribute) ReferenceRecord (class in lamindb.models) references (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.Project attribute) (lamindb.Record attribute) (lamindb.Reference attribute) (lamindb.Transform attribute) refresh_from_db() (bionty.CellLine method) (bionty.CellMarker method) (bionty.CellType method) (bionty.DevelopmentalStage method) (bionty.Disease method) (bionty.Ethnicity method) (bionty.ExperimentalFactor method) (bionty.Gene method) (bionty.Organism method) (bionty.Pathway method) (bionty.Phenotype method) (bionty.Protein method) (bionty.Source method) (bionty.Tissue method) (lamindb.Artifact method) (lamindb.Branch method) (lamindb.Collection method) (lamindb.Feature method) (lamindb.Project method) (lamindb.Record method) (lamindb.Reference method) (lamindb.Run method) (lamindb.Schema method) (lamindb.Space method) (lamindb.Storage method) (lamindb.Transform method) (lamindb.ULabel method) (lamindb.User method) region (lamindb.setup.core.StorageSettings property) (lamindb.Storage attribute) Registry (class in lamindb.models) RelatedManager (class in lamindb.models) relative_to() (lamindb.UPath method) remove() (lamindb.models.RelatedManager method) (lamindb.models.SchemaOptionals method) remove_optional_features() (lamindb.Schema method) remove_synonym() (bionty.CellLine method) (bionty.CellMarker method) (bionty.CellType method) (bionty.DevelopmentalStage method) (bionty.Disease method) (bionty.Ethnicity method) (bionty.ExperimentalFactor method) (bionty.Gene method) (bionty.Organism method) (bionty.Pathway method) (bionty.Phenotype method) (bionty.Protein method) (bionty.Tissue method) (lamindb.Feature method) (lamindb.models.CanCurate method) (lamindb.Project method) (lamindb.Record method) (lamindb.Reference method) (lamindb.Schema method) (lamindb.ULabel method) (lamindb.User method) remove_values() (lamindb.models.FeatureManager method) rename() (lamindb.UPath method) replace() (lamindb.Artifact method) (lamindb.UPath method) report (lamindb.Run attribute) require_organism() (bionty.CellLine class method) (bionty.CellMarker class method) (bionty.CellType class method) (bionty.core.BioRecord class method) (bionty.DevelopmentalStage class method) (bionty.Disease class method) (bionty.Ethnicity class method) (bionty.ExperimentalFactor class method) (bionty.Gene class method) (bionty.models.BioRecord class method) (bionty.Organism class method) (bionty.Pathway class method) (bionty.Phenotype class method) (bionty.Protein class method) (bionty.Tissue class method) resolve() (lamindb.UPath method) restore() (bionty.CellLine method) (bionty.CellMarker method) (bionty.CellType method) (bionty.DevelopmentalStage method) (bionty.Disease method) (bionty.Ethnicity method) (bionty.ExperimentalFactor method) (bionty.Gene method) (bionty.Organism method) (bionty.Pathway method) (bionty.Phenotype method) (bionty.Protein method) (bionty.Source method) (bionty.Tissue method) (lamindb.Artifact method) (lamindb.Collection method) (lamindb.Feature method) (lamindb.models.SQLRecord method) (lamindb.Project method) (lamindb.Record method) (lamindb.Reference method) (lamindb.Run method) (lamindb.Schema method) (lamindb.Storage method) (lamindb.Transform method) (lamindb.ULabel method) rglob() (lamindb.UPath method) rmdir() (lamindb.UPath method) root (lamindb.setup.core.StorageSettings property) (lamindb.Storage attribute) (lamindb.UPath property) root_as_str (lamindb.setup.core.StorageSettings property) run (bionty.CellLine attribute) (bionty.CellMarker attribute) (bionty.CellType attribute) (bionty.DevelopmentalStage attribute) (bionty.Disease attribute) (bionty.Ethnicity attribute) (bionty.ExperimentalFactor attribute) (bionty.Gene attribute) (bionty.Organism attribute) (bionty.Pathway attribute) (bionty.Phenotype attribute) (bionty.Protein attribute) (bionty.Source attribute) (bionty.Tissue attribute) Run (class in lamindb) run (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.core.Context property) Run (lamindb.DB attribute) run (lamindb.Feature attribute) (lamindb.models.RunBlock attribute) (lamindb.models.RunJsonValue attribute) (lamindb.models.RunProject attribute) (lamindb.models.RunRecord attribute) (lamindb.models.RunULabel attribute) (lamindb.models.TracksRun attribute) (lamindb.Project attribute) (lamindb.Record attribute) (lamindb.Reference attribute) (lamindb.Schema attribute) (lamindb.Storage attribute) (lamindb.ULabel attribute) run_id (lamindb.models.TracksRun attribute) RunBlock (class in lamindb.models) RunJsonValue (class in lamindb.models) RunProject (class in lamindb.models) RunRecord (class in lamindb.models) runs (lamindb.Artifact attribute) (lamindb.models.JsonValue attribute) (lamindb.Project attribute) (lamindb.Record attribute) (lamindb.Transform attribute) (lamindb.ULabel attribute) RunULabel (class in lamindb.models) S samefile() (lamindb.UPath method) save() (bionty.CellLine method) (bionty.CellMarker method) (bionty.CellType method) (bionty.core.BioRecord method) (bionty.DevelopmentalStage method) (bionty.Disease method) (bionty.Ethnicity method) (bionty.ExperimentalFactor method) (bionty.Gene method) (bionty.models.BioRecord method) (bionty.Organism method) (bionty.Pathway method) (bionty.Phenotype method) (bionty.Protein method) (bionty.Source method) (bionty.Tissue method) (in module lamindb) (lamindb.Artifact method) (lamindb.Branch method) (lamindb.Collection method) (lamindb.Feature method) (lamindb.models.BaseSQLRecord method) (lamindb.models.LazyArtifact method) (lamindb.Project method) (lamindb.Record method) (lamindb.Reference method) (lamindb.Run method) (lamindb.Schema method) (lamindb.Space method) (lamindb.Storage method) (lamindb.Transform method) (lamindb.ULabel method) (lamindb.User method) (pertdb.Compound method) save_artifact() (lamindb.curators.core.Curator method) (lamindb.curators.core.SlotsCurator method) (lamindb.curators.DataFrameCurator method) save_cellxgene_defaults() (in module lamindb.examples.cellxgene) save_lightning_features() (in module lamindb.integrations.lightning) save_mini_immuno_datasets() (in module lamindb.examples.datasets.mini_immuno) save_mlflow_features() (in module lamindb.examples.mlflow) save_tiledbsoma_experiment() (in module lamindb.integrations) save_vitessce_config() (in module lamindb.integrations) save_wandb_features() (in module lamindb.examples.wandb) SaveConfigCallback (class in lamindb.integrations.lightning) Schema (class in lamindb) schema (lamindb.Artifact attribute) Schema (lamindb.DB attribute) schema (lamindb.models.ArtifactSchema attribute) (lamindb.models.SchemaBlock attribute) (lamindb.models.SchemaFeature attribute) (lamindb.models.SchemaProject attribute) (lamindb.Record attribute) SchemaBlock (class in lamindb.models) SchemaComponent (class in lamindb.models) SchemaFeature (class in lamindb.models) SchemaOptionals (class in lamindb.models) SchemaProject (class in lamindb.models) schemas (bionty.CellMarker attribute) (bionty.Gene attribute) (bionty.Pathway attribute) (bionty.Protein attribute) (lamindb.Artifact attribute) (lamindb.Feature attribute) (lamindb.Project attribute) (lamindb.Schema attribute) schmidt22_crispra_gws_IFNG() (in module lamindb.examples.datasets) schmidt22_perturbseq() (in module lamindb.examples.datasets) scientific_name (bionty.Organism attribute) search() (bionty.CellLine class method) (bionty.CellMarker class method) (bionty.CellType class method) (bionty.DevelopmentalStage class method) (bionty.Disease class method) (bionty.Ethnicity class method) (bionty.ExperimentalFactor class method) (bionty.Gene class method) (bionty.Organism class method) (bionty.Pathway class method) (bionty.Phenotype class method) (bionty.Protein class method) (bionty.Source class method) (bionty.Tissue class method) (lamindb.Artifact class method) (lamindb.Branch class method) (lamindb.Collection class method) (lamindb.Feature class method) (lamindb.models.BaseSQLRecord class method) (lamindb.models.QueryManager method) (lamindb.Project class method) (lamindb.Record class method) (lamindb.Reference class method) (lamindb.Run class method) (lamindb.Schema class method) (lamindb.Space class method) (lamindb.Storage class method) (lamindb.Transform class method) (lamindb.ULabel class method) (lamindb.User class method) search_names (lamindb.core.subsettings.CreationSettings attribute) sequence (pertdb.GeneticPerturbation attribute) set() (lamindb.models.RelatedManager method) (lamindb.models.SchemaOptionals method) set_abbr() (bionty.CellLine method) (bionty.CellMarker method) (bionty.CellType method) (bionty.DevelopmentalStage method) (bionty.Disease method) (bionty.Ethnicity method) (bionty.ExperimentalFactor method) (bionty.Gene method) (bionty.Organism method) (bionty.Pathway method) (bionty.Phenotype method) (bionty.Protein method) (bionty.Tissue method) (lamindb.Feature method) (lamindb.models.CanCurate method) (lamindb.Project method) (lamindb.Record method) (lamindb.Reference method) (lamindb.Schema method) (lamindb.ULabel method) (lamindb.User method) set_values() (lamindb.models.FeatureManager method) Settings (class in bionty.core) (class in lamindb.core) settings (in module bionty) (in module bionty.base) (in module lamindb) (in module lamindb.setup) settings_dir (lamindb.setup.core.SetupSettings property) SettingsEnvFileOutdated setup() (lamindb.integrations.lightning.Checkpoint method) (lamindb.integrations.lightning.SaveConfigCallback method) SetupSettings (class in lamindb.setup.core) shape (lamindb.core.MappedCollection property) show() (lamindb.setup.migrate class method) size (lamindb.Artifact attribute) slot (lamindb.models.ArtifactSchema attribute) (lamindb.models.SchemaComponent attribute) slots (lamindb.curators.core.SlotsCurator property) (lamindb.models.FeatureManager property) (lamindb.Schema property) SlotsCurator (class in lamindb.curators.core) slug (lamindb.setup.core.InstanceSettings property) SlugField (class in lamindb.base.fields) SmallIntegerField (class in lamindb.base.fields) smiles (pertdb.Compound attribute) source (bionty.CellLine attribute) (bionty.CellMarker attribute) (bionty.CellType attribute) (bionty.DevelopmentalStage attribute) (bionty.Disease attribute) (bionty.Ethnicity attribute) (bionty.ExperimentalFactor attribute) (bionty.Gene attribute) (bionty.models.HasSource attribute) (bionty.Organism attribute) (bionty.Pathway attribute) (bionty.Phenotype attribute) (bionty.Protein attribute) (bionty.Tissue attribute) Source (class in bionty) source() (in module bionty.uids) source_code (lamindb.Transform attribute) source_id (bionty.models.HasSource attribute) source_website (bionty.Source attribute) space (bionty.CellLine attribute) (bionty.CellMarker attribute) (bionty.CellType attribute) (bionty.DevelopmentalStage attribute) (bionty.Disease attribute) (bionty.Ethnicity attribute) (bionty.ExperimentalFactor attribute) (bionty.Gene attribute) (bionty.Organism attribute) (bionty.Pathway attribute) (bionty.Phenotype attribute) (bionty.Protein attribute) (bionty.Source attribute) (bionty.Tissue attribute) Space (class in lamindb) space (lamindb.Artifact attribute) (lamindb.Branch attribute) (lamindb.Collection attribute) (lamindb.core.Context property) Space (lamindb.DB attribute) space (lamindb.Feature attribute) (lamindb.models.SpaceBlock attribute) (lamindb.models.SQLRecord attribute) (lamindb.Project attribute) (lamindb.Record attribute) (lamindb.Reference attribute) (lamindb.Run attribute) (lamindb.Schema attribute) (lamindb.setup.core.SetupSettings property) (lamindb.Storage attribute) (lamindb.Transform attribute) (lamindb.ULabel attribute) SpaceBlock (class in lamindb.models) spatialdata_blobs() (in module lamindb.examples.datasets) SpatialDataAccessor (class in lamindb.core.storage) SpatialDataCurator (class in lamindb.curators) SQLRecord (class in lamindb.models) squash() (lamindb.setup.migrate class method) stable_id (bionty.Gene attribute) standardize() (bionty.CellLine class method) (bionty.CellMarker class method) (bionty.CellType class method) (bionty.DevelopmentalStage class method) (bionty.Disease class method) (bionty.Ethnicity class method) (bionty.ExperimentalFactor class method) (bionty.Gene class method) (bionty.Organism class method) (bionty.Pathway class method) (bionty.Phenotype class method) (bionty.Protein class method) (bionty.Tissue class method) (lamindb.curators.core.CatVector method) (lamindb.curators.core.ComponentCurator method) (lamindb.curators.core.DataFrameCatManager method) (lamindb.curators.DataFrameCurator method) (lamindb.Feature class method) (lamindb.models.CanCurate method) (lamindb.Project class method) (lamindb.Record class method) (lamindb.Reference class method) (lamindb.Schema class method) (lamindb.ULabel class method) (lamindb.User class method) start_date (lamindb.Project attribute) started_at (lamindb.Run attribute) stat() (lamindb.UPath method) StaticReference (class in bionty.core) status (lamindb.Run property) stem (lamindb.UPath property) stem_uid (lamindb.Artifact property) (lamindb.Collection property) (lamindb.models.IsVersioned property) (lamindb.Transform property) step() (in module lamindb) Storage (class in lamindb) storage (lamindb.Artifact attribute) (lamindb.core.Settings property) Storage (lamindb.DB attribute) storage (lamindb.setup.core.InstanceSettings property) (lamindb.setup.core.SetupSettings property) storage_options (lamindb.UPath property) StorageAlreadyManaged StorageNotEmpty StorageSettings (class in lamindb.setup.core) StorageType (in module lamindb.setup.types) StrField (in module lamindb.base.types) strict_classmethod() (in module lamindb.base.utils) successor (lamindb.models.TransformTransform attribute) successors (lamindb.Project attribute) (lamindb.Transform attribute) suffix (lamindb.Artifact attribute) (lamindb.UPath property) suffixes (lamindb.UPath property) SUPPORTED_SUFFIXES (in module lamindb.core.loaders) symbol (bionty.Gene attribute) symlink_to() (lamindb.UPath method) sync_git_repo (lamindb.core.Settings property) synchronize_to() (lamindb.UPath method) synonyms (bionty.CellLine attribute) (bionty.CellMarker attribute) (bionty.CellType attribute) (bionty.core.BioRecord attribute) (bionty.DevelopmentalStage attribute) (bionty.Disease attribute) (bionty.Ethnicity attribute) (bionty.ExperimentalFactor attribute) (bionty.Gene attribute) (bionty.models.BioRecord attribute) (bionty.Organism attribute) (bionty.Pathway attribute) (bionty.Phenotype attribute) (bionty.Protein attribute) (bionty.Tissue attribute) (lamindb.Feature attribute) synonyms_mapper (lamindb.models.InspectResult property) T targets (pertdb.Biologic attribute) (pertdb.Compound attribute) (pertdb.EnvironmentalPerturbation attribute) (pertdb.GeneticPerturbation attribute) text (lamindb.Reference attribute) TextField (class in lamindb.base.fields) TiledbsomaExperimentCurator (class in lamindb.curators) TimeField (class in lamindb.base.fields) Tissue (class in bionty) (class in bionty.base) to_artifact() (lamindb.Record method) to_dataframe() (bionty.CellLine class method) (bionty.CellMarker class method) (bionty.CellType class method) (bionty.DevelopmentalStage class method) (bionty.Disease class method) (bionty.Ethnicity class method) (bionty.ExperimentalFactor class method) (bionty.Gene class method) (bionty.Organism class method) (bionty.Pathway class method) (bionty.Phenotype class method) (bionty.Protein class method) (bionty.Source class method) (bionty.Tissue class method) (lamindb.Artifact class method) (lamindb.Branch class method) (lamindb.Collection class method) (lamindb.Feature class method) (lamindb.models.BaseSQLRecord class method) (lamindb.models.QueryManager method) (lamindb.Project class method) (lamindb.Record method) (lamindb.Reference class method) (lamindb.Run class method) (lamindb.Schema class method) (lamindb.Space class method) (lamindb.Storage class method) (lamindb.Transform class method) (lamindb.ULabel class method) (lamindb.User class method) to_list() (lamindb.models.QueryManager method) to_url() (lamindb.UPath method) torch_worker_init_fn() (lamindb.core.MappedCollection class method) touch() (lamindb.UPath method) track() (in module lamindb) track_run_inputs (lamindb.core.Settings attribute) TracksRun (class in lamindb.models) TracksUpdates (class in lamindb.models) Transform (class in lamindb) transform (lamindb.Artifact property) (lamindb.Collection property) (lamindb.core.Context property) Transform (lamindb.DB attribute) transform (lamindb.models.TransformBlock attribute) (lamindb.models.TransformProject attribute) (lamindb.models.TransformRecord attribute) (lamindb.models.TransformReference attribute) (lamindb.models.TransformULabel attribute) (lamindb.Run attribute) TransformBlock (class in lamindb.models) TransformKind (in module lamindb.base.types) TransformProject (class in lamindb.models) TransformRecord (class in lamindb.models) TransformReference (class in lamindb.models) transforms (lamindb.Project attribute) (lamindb.Record attribute) (lamindb.Reference attribute) (lamindb.ULabel attribute) TransformTransform (class in lamindb.models) TransformULabel (class in lamindb.models) type (lamindb.Feature attribute) (lamindb.Project attribute) (lamindb.Record attribute) (lamindb.Reference attribute) (lamindb.Schema attribute) (lamindb.setup.core.StorageSettings property) (lamindb.Storage attribute) (lamindb.ULabel attribute) (pertdb.Biologic attribute) (pertdb.Compound attribute) (pertdb.GeneticPerturbation attribute) type_is_cloud (lamindb.setup.core.StorageSettings property) U ui_url (lamindb.setup.core.InstanceSettings property) uid (bionty.CellLine attribute) (bionty.CellMarker attribute) (bionty.CellType attribute) (bionty.core.BioRecord attribute) (bionty.DevelopmentalStage attribute) (bionty.Disease attribute) (bionty.Ethnicity attribute) (bionty.ExperimentalFactor attribute) (bionty.Gene attribute) (bionty.models.BioRecord attribute) (bionty.Organism attribute) (bionty.Pathway attribute) (bionty.Phenotype attribute) (bionty.Protein attribute) (bionty.Source attribute) (bionty.Tissue attribute) (lamindb.Artifact attribute) (lamindb.Branch attribute) (lamindb.Collection attribute) (lamindb.core.Context property) (lamindb.Feature attribute) (lamindb.Project attribute) (lamindb.Record attribute) (lamindb.Reference attribute) (lamindb.Run attribute) (lamindb.Schema attribute) (lamindb.setup.core.InstanceSettings property) (lamindb.setup.core.StorageSettings property) (lamindb.setup.core.UserSettings attribute) (lamindb.Space attribute) (lamindb.Storage attribute) (lamindb.Transform attribute) (lamindb.ULabel attribute) (lamindb.User attribute) ULabel (class in lamindb) (lamindb.DB attribute) ulabel (lamindb.models.ArtifactULabel attribute) (lamindb.models.CollectionULabel attribute) (lamindb.models.RunULabel attribute) (lamindb.models.TransformULabel attribute) (lamindb.models.ULabelBlock attribute) (lamindb.models.ULabelProject attribute) ULabelBlock (class in lamindb.models) ULabelProject (class in lamindb.models) ulabels (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.Project attribute) (lamindb.Run attribute) (lamindb.Transform attribute) (lamindb.ULabel attribute) uniprotkb_id (bionty.CellMarker attribute) (bionty.Protein attribute) unit (lamindb.Feature attribute) (pertdb.EnvironmentalPerturbation attribute) UnknownStorageLocation unlink() (lamindb.UPath method) UPath (class in lamindb) UPathStr (in module lamindb.base.types) (in module lamindb.setup.types) update_smiles() (pertdb.Compound method) UpdateContext updated_at (bionty.CellLine attribute) (bionty.CellMarker attribute) (bionty.CellType attribute) (bionty.DevelopmentalStage attribute) (bionty.Disease attribute) (bionty.Ethnicity attribute) (bionty.ExperimentalFactor attribute) (bionty.Gene attribute) (bionty.Organism attribute) (bionty.Pathway attribute) (bionty.Phenotype attribute) (bionty.Protein attribute) (bionty.Source attribute) (bionty.Tissue attribute) (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.Feature attribute) (lamindb.Project attribute) (lamindb.Record attribute) (lamindb.Reference attribute) (lamindb.Run attribute) (lamindb.Schema attribute) (lamindb.Storage attribute) (lamindb.Transform attribute) (lamindb.ULabel attribute) (lamindb.User attribute) upload_from() (lamindb.UPath method) url (bionty.Source attribute) (lamindb.Project attribute) (lamindb.Reference attribute) URLField (class in lamindb.base.fields) User (class in lamindb) (lamindb.DB attribute) user (lamindb.models.ArtifactUser attribute) (lamindb.setup.core.SetupSettings property) users (lamindb.Artifact attribute) UserSettings (class in lamindb.setup.core) UUIDField (class in lamindb.base.fields) V valid_features() (in module lamindb.examples.schemas) VALID_SUFFIXES (in module lamindb.core.storage) validate() (bionty.CellLine class method) (bionty.CellMarker class method) (bionty.CellType class method) (bionty.DevelopmentalStage class method) (bionty.Disease class method) (bionty.Ethnicity class method) (bionty.ExperimentalFactor class method) (bionty.Gene class method) (bionty.Organism class method) (bionty.Pathway class method) (bionty.Phenotype class method) (bionty.Protein class method) (bionty.Tissue class method) (lamindb.curators.core.CatVector method) (lamindb.curators.core.ComponentCurator method) (lamindb.curators.core.Curator method) (lamindb.curators.core.DataFrameCatManager method) (lamindb.curators.core.SlotsCurator method) (lamindb.curators.DataFrameCurator method) (lamindb.Feature class method) (lamindb.models.CanCurate method) (lamindb.Project class method) (lamindb.Record class method) (lamindb.Reference class method) (lamindb.Schema class method) (lamindb.ULabel class method) (lamindb.User class method) validated (lamindb.models.InspectResult property) validated_artifacts (lamindb.Schema attribute) ValidateFields (class in lamindb.models) ValidationError value (lamindb.models.ArtifactArtifact attribute) (lamindb.models.JsonValue attribute) (lamindb.models.RecordArtifact attribute) (lamindb.models.RecordCollection attribute) (lamindb.models.RecordJson attribute) (lamindb.models.RecordProject attribute) (lamindb.models.RecordRecord attribute) (lamindb.models.RecordReference attribute) (lamindb.models.RecordRun attribute) (lamindb.models.RecordTransform attribute) (lamindb.models.RecordULabel attribute) (lamindb.models.RecordUser attribute) (pertdb.EnvironmentalPerturbation attribute) values (lamindb.curators.core.CatVector property) (lamindb.Feature attribute) values_artifact (lamindb.Record attribute) values_collection (lamindb.Record attribute) values_json (lamindb.Record attribute) values_project (lamindb.Record attribute) values_record (lamindb.Record attribute) values_reference (lamindb.Record attribute) values_run (lamindb.Record attribute) values_transform (lamindb.Record attribute) values_ulabel (lamindb.Record attribute) values_user (lamindb.Record attribute) vendor (lamindb.setup.core.InstanceSettings property) verbosity (lamindb.core.Settings property) version (bionty.Source attribute) (lamindb.Artifact property) (lamindb.Collection property) (lamindb.core.Context property) (lamindb.models.IsVersioned property) (lamindb.Transform property) version_tag (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.Transform attribute) versions (lamindb.Artifact property) (lamindb.Collection property) (lamindb.models.IsVersioned property) (lamindb.Transform property) view() (in module lamindb) view_children() (bionty.CellLine method) (bionty.CellType method) (bionty.DevelopmentalStage method) (bionty.Disease method) (bionty.Ethnicity method) (bionty.ExperimentalFactor method) (bionty.Organism method) (bionty.Pathway method) (bionty.Phenotype method) (bionty.Tissue method) (lamindb.models.HasParents method) (lamindb.Record method) (lamindb.ULabel method) view_lineage() (lamindb.Artifact method) (lamindb.Collection method) (lamindb.Transform method) view_parents() (bionty.CellLine method) (bionty.CellType method) (bionty.DevelopmentalStage method) (bionty.Disease method) (bionty.Ethnicity method) (bionty.ExperimentalFactor method) (bionty.Organism method) (bionty.Pathway method) (bionty.Phenotype method) (bionty.Tissue method) (lamindb.models.HasParents method) (lamindb.Record method) (lamindb.ULabel method) view_tree() (lamindb.UPath method) W walk() (lamindb.UPath method) with_config() (lamindb.Feature method) with_name() (lamindb.UPath method) with_segments() (lamindb.UPath method) with_stem() (lamindb.UPath method) with_suffix() (lamindb.UPath method) write_bytes() (lamindb.UPath method) write_text() (lamindb.UPath method)