Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | Z A abbr (bionty.CellLine attribute) (bionty.CellType attribute) (bionty.DevelopmentalStage attribute) (bionty.Disease attribute) (bionty.Ethnicity attribute) (bionty.ExperimentalFactor attribute) (bionty.Pathway attribute) (bionty.Phenotype attribute) (bionty.Tissue attribute) absolute() (lamindb.UPath method) access_token (lamindb.setup.core.UserSettings attribute) accessor (lamindb.Artifact attribute) add() (lamindb.core.LabelManager method) add_feature_set() (lamindb.core.FeatureManager method) add_from() (lamindb.core.LabelManager method) add_new_from() (lamindb.core.DataFrameAnnotator method) (lamindb.core.MuDataAnnotator method) add_new_from_columns() (lamindb.core.DataFrameAnnotator method) (lamindb.core.MuDataAnnotator method) add_new_from_var_index() (lamindb.core.AnnDataAnnotator method) (lamindb.core.MuDataAnnotator method) add_synonym() (lamindb.core.CanValidate method) add_to_version_family() (lamindb.core.IsVersioned method) add_validated_from() (lamindb.core.DataFrameAnnotator method) (lamindb.core.MuDataAnnotator method) add_values() (lamindb.core.FeatureManager method) (lamindb.core.ParamManager method) all() (lamindb.core.QueryManager method) anchor (lamindb.UPath attribute) anndata_file_pbmc68k_test() (in module lamindb.core.datasets) anndata_human_immune_cells() (in module lamindb.core.datasets) anndata_mouse_sc_lymph_node() (in module lamindb.core.datasets) anndata_pbmc3k_processed() (in module lamindb.core.datasets) anndata_pbmc68k_reduced() (in module lamindb.core.datasets) anndata_suo22_Visium10X() (in module lamindb.core.datasets) anndata_with_obs() (in module lamindb.core.datasets) AnnDataAccessor (class in lamindb.core.storage) AnnDataAnnotator (class in lamindb.core) Annotate (class in lamindb) AnnotateLookup (class in lamindb.core) args (lamindb.core.exceptions.MissingTransformSettings attribute) (lamindb.core.exceptions.NotebookNotSavedError attribute) (lamindb.core.exceptions.NoTitleError attribute) (lamindb.core.exceptions.UpdateTransformSettings attribute) (lamindb.core.exceptions.ValidationError attribute) Artifact (class in lamindb) artifact (lamindb.Collection attribute) artifact_set (lamindb.User attribute) artifact_use_virtual_keys (lamindb.core.Settings attribute) artifactcellline_set (lamindb.Run attribute) (lamindb.User attribute) artifactcellmarker_set (lamindb.Run attribute) (lamindb.User attribute) artifactcelltype_set (lamindb.Run attribute) (lamindb.User attribute) artifactdevelopmentalstage_set (lamindb.Run attribute) (lamindb.User attribute) artifactdisease_set (lamindb.Run attribute) (lamindb.User attribute) artifactethnicity_set (lamindb.Run attribute) (lamindb.User attribute) artifactexperimentalfactor_set (lamindb.Run attribute) (lamindb.User attribute) artifactfeatureset_set (lamindb.Run attribute) (lamindb.User attribute) artifactfeaturevalue_set (lamindb.Run attribute) (lamindb.User attribute) artifactgene_set (lamindb.Run attribute) (lamindb.User attribute) artifactorganism_set (lamindb.Run attribute) (lamindb.User attribute) artifactpathway_set (lamindb.Run attribute) (lamindb.User attribute) artifactphenotype_set (lamindb.Run attribute) (lamindb.User attribute) artifactprotein_set (lamindb.Run attribute) (lamindb.User attribute) 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.Tissue attribute) (lamindb.Collection attribute) (wetlab.Experiment attribute) (wetlab.Treatment attribute) (wetlab.TreatmentTarget attribute) (wetlab.Well attribute) artifacttissue_set (lamindb.Run attribute) (lamindb.User attribute) artifactulabel_set (lamindb.Run attribute) (lamindb.User attribute) as_uri() (lamindb.UPath method) auto_connect (lamindb.setup.core.SetupSettings attribute) auto_created (lamindb.core.QueryManager attribute) auto_save_parents (bionty.core.Settings attribute) B backed() (lamindb.Artifact method) BackedAccessor (class in lamindb.core.storage) batch (wetlab.Biosample attribute) (wetlab.Techsample attribute) bionty module bionty.core module BioRegistry (class in bionty.core) Biosample (class in wetlab) biosamples (wetlab.Techsample attribute) biotype (bionty.Gene attribute) C cache() (lamindb.Artifact method) (lamindb.Collection method) cache_dir (lamindb.setup.core.StorageSettings attribute) CanValidate (class in lamindb.core) capitalize() (lamindb.core.types.TransformType method) casefold() (lamindb.core.types.TransformType method) categoricals (lamindb.core.AnnDataAnnotator attribute) (lamindb.core.MuDataAnnotator attribute) cell_lines (wetlab.Biosample attribute) cell_types (wetlab.Biosample attribute) CellLine (class in bionty) cellline_set (lamindb.Run attribute) (lamindb.User attribute) CellMarker (class in bionty) cellmarker_set (lamindb.Run attribute) (lamindb.User attribute) CellType (class in bionty) celltype_set (lamindb.Run attribute) (lamindb.User attribute) center() (lamindb.core.types.TransformType method) check() (lamindb.setup.migrate class method) chmod() (lamindb.UPath method) choices() (lamindb.core.types.TransformType class method) clean_up_failed_runs() (lamindb.core.DataFrameAnnotator method) close() (in module lamindb.setup) (lamindb.core.MappedCollection method) (lamindb.core.storage.AnnDataAccessor method) closed (lamindb.core.MappedCollection attribute) (lamindb.core.storage.AnnDataAccessor attribute) cloud_to_local() (lamindb.setup.core.StorageSettings method) cloud_to_local_no_update() (lamindb.setup.core.StorageSettings method) code (lamindb.core.exceptions.MissingTransformSettings attribute) (lamindb.core.exceptions.UpdateTransformSettings attribute) (lamindb.core.exceptions.ValidationError attribute) Collection (class in lamindb) collection_set (lamindb.User attribute) collectionartifact_set (lamindb.Run attribute) (lamindb.User attribute) collectionfeatureset_set (lamindb.Run attribute) (lamindb.User attribute) collections (wetlab.Biosample attribute) (wetlab.Experiment attribute) (wetlab.Treatment attribute) (wetlab.Well attribute) collectionulabel_set (lamindb.Run attribute) (lamindb.User attribute) column (wetlab.Well attribute) connect() (in module lamindb) count() (lamindb.core.types.TransformType method) create() (lamindb.setup.migrate class method) 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.PublicSource attribute) (bionty.Tissue attribute) (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.core.TracksRun attribute) (lamindb.Feature attribute) (lamindb.FeatureSet attribute) (lamindb.Param attribute) (lamindb.Run attribute) (lamindb.Storage attribute) (lamindb.Transform attribute) (lamindb.ULabel attribute) (lamindb.User attribute) (wetlab.Biosample attribute) (wetlab.Experiment attribute) (wetlab.ExperimentType attribute) (wetlab.Techsample attribute) (wetlab.Treatment attribute) (wetlab.TreatmentTarget attribute) (wetlab.Well 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.PublicSource attribute) (bionty.Tissue attribute) (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.core.TracksRun attribute) (lamindb.Feature attribute) (lamindb.FeatureSet attribute) (lamindb.Param attribute) (lamindb.Run attribute) (lamindb.Storage attribute) (lamindb.Transform attribute) (lamindb.ULabel attribute) (wetlab.Experiment attribute) (wetlab.ExperimentType attribute) (wetlab.Techsample attribute) (wetlab.Treatment attribute) (wetlab.TreatmentTarget attribute) (wetlab.Well attribute) creation_counter (lamindb.core.QueryManager attribute) currently_used (bionty.PublicSource attribute) cwd() (lamindb.UPath class method) D DataFrameAnnotator (class in lamindb.core) date (wetlab.Experiment attribute) db (lamindb.core.QueryManager attribute) (lamindb.core.QuerySet attribute) (lamindb.setup.core.InstanceSettings attribute) defined_migrations() (lamindb.setup.migrate class method) delete() (in module lamindb.setup) (lamindb.Artifact method) (lamindb.Collection method) (lamindb.core.QuerySet method) (lamindb.Run method) (lamindb.Transform method) deploy() (lamindb.setup.migrate class method) deployed_migrations() (lamindb.setup.migrate class method) describe() (lamindb.core.HasFeatures method) description (bionty.CellLine attribute) (bionty.CellType attribute) (bionty.DevelopmentalStage attribute) (bionty.Disease attribute) (bionty.Ethnicity attribute) (bionty.ExperimentalFactor attribute) (bionty.Gene attribute) (bionty.Pathway attribute) (bionty.Phenotype attribute) (bionty.Tissue attribute) (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.Feature attribute) (lamindb.Storage attribute) (lamindb.Transform attribute) (lamindb.ULabel attribute) (wetlab.Biosample attribute) (wetlab.Experiment attribute) (wetlab.ExperimentType attribute) (wetlab.Techsample attribute) (wetlab.Treatment attribute) (wetlab.TreatmentTarget attribute) DevelopmentalStage (class in bionty) developmentalstage_set (lamindb.Run attribute) (lamindb.User attribute) df (lamindb.core.InspectResult attribute) df() (bionty.core.PublicOntology method) (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) (lamindb.core.RecordsList method) (lamindb.core.Registry class method) df_iris() (in module lamindb.core.datasets) df_iris_in_meter() (in module lamindb.core.datasets) df_iris_in_meter_study1() (in module lamindb.core.datasets) df_iris_in_meter_study2() (in module lamindb.core.datasets) dialect (lamindb.setup.core.InstanceSettings attribute) diff() (bionty.core.PublicOntology method) dir_iris_images() (in module lamindb.core.datasets) dir_scrnaseq_cellranger() (in module lamindb.core.datasets) Disease (class in bionty) disease_set (lamindb.Run attribute) (lamindb.User attribute) diseases (wetlab.Biosample attribute) django() (in module lamindb.setup) download_to() (lamindb.UPath method) drive (lamindb.UPath attribute) dtype (lamindb.Feature attribute) (lamindb.FeatureSet attribute) (lamindb.Param attribute) E email (lamindb.setup.core.UserSettings attribute) encode() (lamindb.core.types.TransformType method) endswith() (lamindb.core.types.TransformType method) ensembl_gene_id (bionty.Gene attribute) ensembl_gene_ids (bionty.Protein attribute) entity (bionty.PublicSource attribute) environment (lamindb.Run attribute) Ethnicity (class in bionty) ethnicity_set (lamindb.Run attribute) (lamindb.User attribute) exists() (lamindb.UPath method) expandtabs() (lamindb.core.types.TransformType method) expanduser() (lamindb.UPath method) Experiment (class in wetlab) experiment_type (wetlab.Experiment attribute) ExperimentalFactor (class in bionty) experimentalfactor_set (lamindb.Run attribute) (lamindb.User attribute) ExperimentType (class in wetlab) F fake_bio_notebook_titles() (in module lamindb.core.datasets) Feature (class in lamindb) feature_set (lamindb.Run attribute) (lamindb.User attribute) feature_sets (bionty.CellMarker attribute) (bionty.Gene attribute) (bionty.Pathway attribute) (bionty.Protein attribute) (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.Feature attribute) feature_values (lamindb.Artifact attribute) FeatureManager (class in lamindb.core) features (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.core.HasFeatures attribute) FeatureSet (class in lamindb) featureset_set (lamindb.Run attribute) (lamindb.User attribute) featurevalue_set (lamindb.Feature attribute) (lamindb.Run attribute) (lamindb.User attribute) FieldAttr (in module lamindb.core.fields) fields (bionty.core.PublicOntology attribute) (lamindb.core.AnnDataAnnotator attribute) (lamindb.core.DataFrameAnnotator attribute) file_bam() (in module lamindb.core.datasets) file_fastq() (in module lamindb.core.datasets) file_fcs() (in module lamindb.core.datasets) file_fcs_alpert19() (in module lamindb.core.datasets) file_jpg_paradisi05() (in module lamindb.core.datasets) file_mini_csv() (in module lamindb.core.datasets) file_tiff_suo22() (in module lamindb.core.datasets) file_tsv_rnaseq_nfcore_salmon_merged_gene_counts() (in module lamindb.core.datasets) filter() (lamindb.core.FeatureManager class method) (lamindb.core.Registry class method) find() (lamindb.core.types.TransformType method) finish() (in module lamindb) finished_at (lamindb.Run attribute) first() (lamindb.core.QuerySet method) format() (lamindb.core.types.TransformType method) format_map() (lamindb.core.types.TransformType method) frac_validated (lamindb.core.InspectResult attribute) from_anndata() (lamindb.Annotate class method) (lamindb.Artifact class method) from_df() (lamindb.Annotate class method) (lamindb.Artifact class method) (lamindb.Feature class method) (lamindb.FeatureSet class method) from_dir() (lamindb.Artifact class method) from_mudata() (lamindb.Annotate class method) (lamindb.Artifact class method) from_public() (bionty.core.BioRegistry class method) from_values() (lamindb.core.Registry class method) (lamindb.FeatureSet class method) fs (lamindb.UPath attribute) function (lamindb.core.types.TransformType attribute) G Gene (class in bionty) gene_set (lamindb.Run attribute) (lamindb.User attribute) gene_symbol (bionty.CellMarker attribute) (bionty.Protein attribute) genes (bionty.Pathway attribute) (wetlab.TreatmentTarget attribute) get() (lamindb.core.LabelManager method) (lamindb.core.Registry class method) get_label_weights() (lamindb.core.MappedCollection method) get_merged_categories() (lamindb.core.MappedCollection method) get_merged_labels() (lamindb.core.MappedCollection method) get_system_display() (wetlab.Treatment method) get_type_display() (lamindb.Artifact method) (lamindb.Transform method) (wetlab.Treatment method) get_values() (lamindb.core.FeatureManager method) (lamindb.core.ParamManager method) git_repo (lamindb.setup.core.InstanceSettings attribute) glob() (lamindb.UPath method) group() (lamindb.UPath method) H handle (lamindb.setup.core.UserSettings attribute) (lamindb.User attribute) hardlink_to() (lamindb.UPath method) HasFeatures (class in lamindb.core) hash (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.FeatureSet attribute) hash_type (lamindb.Artifact attribute) HasParams (class in lamindb.core) HasParents (class in lamindb.core) home() (lamindb.UPath class method) I id (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.PublicSource attribute) (bionty.Tissue attribute) (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.Feature attribute) (lamindb.FeatureSet attribute) (lamindb.Param attribute) (lamindb.Run attribute) (lamindb.setup.core.StorageSettings attribute) (lamindb.setup.core.UserSettings attribute) (lamindb.Storage attribute) (lamindb.Transform attribute) (lamindb.ULabel attribute) (lamindb.User attribute) (wetlab.Biosample attribute) (wetlab.Experiment attribute) (wetlab.ExperimentType attribute) (wetlab.Techsample attribute) (wetlab.Treatment attribute) (wetlab.TreatmentTarget attribute) (wetlab.Well attribute) index() (lamindb.core.types.TransformType method) init() (in module lamindb.setup) input_of (lamindb.Artifact attribute) (lamindb.Collection attribute) inspect() (bionty.core.PublicOntology method) (lamindb.core.CanValidate class method) (lamindb.core.QuerySet method) InspectResult (class in lamindb.core) instance (lamindb.setup.core.SetupSettings attribute) instance_uid (lamindb.Storage attribute) InstanceSettings (class in lamindb.setup.core) instrument (bionty.ExperimentalFactor attribute) is_block_device() (lamindb.UPath method) is_char_device() (lamindb.UPath method) is_consecutive (lamindb.Run attribute) is_dir() (lamindb.UPath method) is_fifo() (lamindb.UPath method) is_file() (lamindb.UPath method) is_junction() (lamindb.UPath method) is_mount() (lamindb.UPath method) is_on_hub (lamindb.setup.core.InstanceSettings attribute) (lamindb.setup.core.StorageSettings attribute) is_relative_to() (lamindb.UPath method) is_remote (lamindb.setup.core.InstanceSettings attribute) is_reserved() (lamindb.UPath method) is_socket() (lamindb.UPath method) is_symlink() (lamindb.UPath method) isalnum() (lamindb.core.types.TransformType method) isalpha() (lamindb.core.types.TransformType method) isascii() (lamindb.core.types.TransformType method) isdecimal() (lamindb.core.types.TransformType method) isdigit() (lamindb.core.types.TransformType method) isidentifier() (lamindb.core.types.TransformType method) islower() (lamindb.core.types.TransformType method) isnumeric() (lamindb.core.types.TransformType method) isprintable() (lamindb.core.types.TransformType method) isspace() (lamindb.core.types.TransformType method) istitle() (lamindb.core.types.TransformType method) isupper() (lamindb.core.types.TransformType method) IsVersioned (class in lamindb.core) iterdir() (lamindb.UPath method) J join() (lamindb.core.types.TransformType method) joinuri() (lamindb.UPath method) K keep_artifacts_local (lamindb.setup.core.InstanceSettings attribute) key (lamindb.Artifact attribute) (lamindb.Transform attribute) key_is_virtual (lamindb.Artifact attribute) key_to_filepath() (lamindb.setup.core.StorageSettings method) L LabelManager (class in lamindb.core) labels (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.core.HasFeatures attribute) lamindb module lamindb.core module lamindb.core.datasets module lamindb.core.exceptions module lamindb.core.fields module lamindb.core.storage module lamindb.core.types module lamindb.integrations module lamindb.setup module lamindb.setup.core module latest_report (lamindb.Transform attribute) latest_run (lamindb.Transform attribute) latest_version() (lamindb.core.QuerySet method) length (bionty.Protein attribute) list() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) ListLike (in module lamindb.core.types) ljust() (lamindb.core.types.TransformType method) load() (lamindb.Artifact method) (lamindb.Collection method) local_filepath() (lamindb.setup.core.StorageSettings method) login() (in module lamindb.setup) logout() (in module lamindb.setup) lookup() (bionty.core.PublicOntology method) (lamindb.core.AnnDataAnnotator method) (lamindb.core.DataFrameAnnotator method) (lamindb.core.MuDataAnnotator method) (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) (lamindb.core.Registry class method) lower() (lamindb.core.types.TransformType method) lstat() (lamindb.UPath method) lstrip() (lamindb.core.types.TransformType method) M maketrans() (lamindb.core.types.TransformType static method) map_synonyms() (bionty.core.PublicOntology method) (lamindb.core.CanValidate class method) mapped() (lamindb.Collection method) MappedCollection (class in lamindb.core) md5 (bionty.PublicSource attribute) measurement (bionty.ExperimentalFactor attribute) members (lamindb.FeatureSet attribute) migrate (class in lamindb.setup) MissingTransformSettings mkdir() (lamindb.UPath method) modified (lamindb.UPath attribute) module bionty bionty.core lamindb lamindb.core lamindb.core.datasets lamindb.core.exceptions lamindb.core.fields lamindb.core.storage lamindb.core.types lamindb.integrations lamindb.setup lamindb.setup.core wetlab molecule (bionty.ExperimentalFactor attribute) mudata_papalexi21_subset() (in module lamindb.core.datasets) MuDataAnnotator (class in lamindb.core) N n (lamindb.FeatureSet attribute) n_empty (lamindb.core.InspectResult attribute) n_objects (lamindb.Artifact attribute) n_observations (lamindb.Artifact attribute) n_unique (lamindb.core.InspectResult attribute) 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.Tissue attribute) (lamindb.Collection attribute) (lamindb.core.types.TransformType attribute) (lamindb.Feature attribute) (lamindb.FeatureSet attribute) (lamindb.Param attribute) (lamindb.setup.core.InstanceSettings attribute) (lamindb.setup.core.UserSettings attribute) (lamindb.Transform attribute) (lamindb.ULabel attribute) (lamindb.UPath attribute) (lamindb.User attribute) (wetlab.Biosample attribute) (wetlab.Experiment attribute) (wetlab.ExperimentType attribute) (wetlab.Techsample attribute) (wetlab.Treatment attribute) (wetlab.TreatmentTarget attribute) (wetlab.Well attribute) ncbi_gene_id (bionty.CellMarker attribute) ncbi_gene_ids (bionty.Gene attribute) non_validated (lamindb.core.InspectResult attribute) notebook (lamindb.core.types.TransformType attribute) NotebookNotSavedError NoTitleError O objects (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.PublicSource attribute) (bionty.Tissue attribute) (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.Feature attribute) (lamindb.FeatureSet attribute) (lamindb.Param attribute) (lamindb.Run attribute) (lamindb.Storage attribute) (lamindb.Transform attribute) (lamindb.ULabel attribute) (lamindb.User attribute) (wetlab.Biosample attribute) (wetlab.Experiment attribute) (wetlab.ExperimentType attribute) (wetlab.Techsample attribute) (wetlab.Treatment attribute) (wetlab.TreatmentTarget attribute) (wetlab.Well attribute) obs_names (lamindb.core.storage.AnnDataAccessor attribute) off_target_score (wetlab.Treatment attribute) on_target_score (wetlab.Treatment attribute) one() (lamindb.core.QuerySet method) (lamindb.core.RecordsList method) one_or_none() (lamindb.core.QuerySet method) 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) (wetlab.ExperimentType attribute) (wetlab.Treatment attribute) open() (lamindb.UPath method) ordered (lamindb.core.QuerySet attribute) organism (bionty.CellMarker attribute) (bionty.core.PublicOntology attribute) (bionty.core.Settings attribute) (bionty.Gene attribute) (bionty.Protein attribute) (bionty.PublicSource attribute) Organism (class in bionty) organism_set (lamindb.Run attribute) (lamindb.User attribute) original_shapes (lamindb.core.MappedCollection attribute) owner (lamindb.setup.core.InstanceSettings attribute) owner() (lamindb.UPath method) P Param (class in lamindb) param_set (lamindb.Run attribute) (lamindb.User attribute) param_values (lamindb.Artifact attribute) (lamindb.Run attribute) ParamManager (class in lamindb.core) params (lamindb.Artifact attribute) (lamindb.core.HasParams attribute) (lamindb.Run attribute) paramvalue_set (lamindb.Param attribute) (lamindb.User attribute) parent (lamindb.UPath attribute) parents (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) (lamindb.Transform attribute) (lamindb.ULabel attribute) (lamindb.UPath attribute) partition() (lamindb.core.types.TransformType method) parts (lamindb.UPath attribute) password (lamindb.setup.core.UserSettings attribute) path (lamindb.Artifact attribute) (lamindb.core.run_context attribute) (lamindb.Storage attribute) (lamindb.UPath attribute) Pathway (class in bionty) pathway_set (lamindb.Run attribute) (lamindb.User attribute) Phenotype (class in bionty) phenotype_set (lamindb.Run attribute) (lamindb.User attribute) pipeline (lamindb.core.types.TransformType attribute) previous_runs (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.PublicSource attribute) (bionty.Tissue attribute) (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.core.TracksUpdates attribute) (lamindb.Feature attribute) (lamindb.Param attribute) (lamindb.Storage attribute) (lamindb.ULabel attribute) Protein (class in bionty) protein_set (lamindb.Run attribute) (lamindb.User attribute) protocol (lamindb.UPath attribute) pubchem_id (wetlab.Treatment attribute) public() (bionty.core.BioRegistry class method) public_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.Organism attribute) (bionty.Pathway attribute) (bionty.Phenotype attribute) (bionty.Protein attribute) (bionty.Tissue attribute) PublicOntology (class in bionty.core) PublicSource (class in bionty) publicsource_set (lamindb.Run attribute) (lamindb.User attribute) Q query (lamindb.core.QuerySet attribute) QueryManager (class in lamindb.core) QuerySet (class in lamindb.core) R readlink() (lamindb.UPath method) record (lamindb.setup.core.StorageSettings attribute) RecordsList (class in lamindb.core) reference (lamindb.Collection attribute) (lamindb.Run attribute) (lamindb.Transform attribute) (lamindb.ULabel attribute) reference_type (lamindb.Collection attribute) (lamindb.Run attribute) (lamindb.Transform attribute) (lamindb.ULabel attribute) region (lamindb.setup.core.StorageSettings attribute) (lamindb.Storage attribute) register() (in module lamindb.setup) Registry (class in lamindb.core) registry (lamindb.FeatureSet attribute) relative_to() (lamindb.UPath method) remove_synonym() (lamindb.core.CanValidate method) removeprefix() (lamindb.core.types.TransformType method) removesuffix() (lamindb.core.types.TransformType method) rename() (lamindb.UPath method) replace() (lamindb.Artifact method) (lamindb.core.types.TransformType method) (lamindb.UPath method) report (lamindb.Run attribute) resolve() (lamindb.UPath method) restore() (lamindb.Artifact method) (lamindb.Collection method) rfind() (lamindb.core.types.TransformType method) rglob() (lamindb.UPath method) rindex() (lamindb.core.types.TransformType method) rjust() (lamindb.core.types.TransformType method) rmdir() (lamindb.UPath method) root (lamindb.setup.core.StorageSettings attribute) (lamindb.Storage attribute) (lamindb.UPath attribute) root_as_str (lamindb.setup.core.StorageSettings attribute) row (wetlab.Well attribute) rpartition() (lamindb.core.types.TransformType method) rsplit() (lamindb.core.types.TransformType method) rstrip() (lamindb.core.types.TransformType method) 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.PublicSource attribute) (bionty.Tissue attribute) Run (class in lamindb) run (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.core.run_context attribute) (lamindb.core.TracksRun attribute) (lamindb.Feature attribute) (lamindb.FeatureSet attribute) (lamindb.Param attribute) (lamindb.Storage attribute) (lamindb.ULabel attribute) run_context (class in lamindb.core) run_set (lamindb.User attribute) S samefile() (lamindb.UPath method) save() (bionty.core.BioRegistry method) (in module lamindb) (lamindb.Artifact method) (lamindb.Collection method) (lamindb.core.Registry method) (lamindb.Feature method) (lamindb.FeatureSet method) save_artifact() (lamindb.core.AnnDataAnnotator method) (lamindb.core.DataFrameAnnotator method) (lamindb.core.MuDataAnnotator method) save_collection() (lamindb.core.DataFrameAnnotator method) save_vitessce_config() (in module lamindb.integrations) schema (lamindb.setup.core.InstanceSettings attribute) schmidt22_crispra_gws_IFNG() (in module lamindb.core.datasets) schmidt22_perturbseq() (in module lamindb.core.datasets) scientific_name (bionty.Organism attribute) script (lamindb.core.types.TransformType attribute) search() (bionty.core.PublicOntology method) (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) (lamindb.core.Registry class method) sequence (wetlab.Treatment attribute) set_abbr() (lamindb.core.CanValidate method) set_as_currently_used() (bionty.PublicSource method) set_latest_public_sources_as_currently_used() (in module bionty.core) Settings (class in bionty.core) (class in lamindb.core) settings (in module bionty) (in module lamindb) (in module lamindb.setup) settings_dir (lamindb.setup.core.SetupSettings attribute) SetupSettings (class in lamindb.setup.core) shape (lamindb.core.MappedCollection attribute) show() (lamindb.setup.migrate class method) silence_file_run_transform_warning (lamindb.core.Settings attribute) size (lamindb.Artifact attribute) slug (lamindb.setup.core.InstanceSettings attribute) source (bionty.core.PublicOntology attribute) (bionty.PublicSource attribute) source_code (lamindb.Transform attribute) source_name (bionty.PublicSource attribute) source_website (bionty.PublicSource attribute) sources() (bionty.core.BioRegistry class method) split() (lamindb.core.types.TransformType method) splitlines() (lamindb.core.types.TransformType method) squash() (lamindb.setup.migrate class method) stable_id (bionty.Gene attribute) stage() (lamindb.Collection method) standardize() (bionty.core.PublicOntology method) (lamindb.core.CanValidate class method) (lamindb.core.QuerySet method) started_at (lamindb.Run attribute) startswith() (lamindb.core.types.TransformType method) stat() (lamindb.UPath method) stem (lamindb.UPath attribute) stem_uid (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.core.IsVersioned attribute) (lamindb.core.TransformSettings attribute) (lamindb.Transform attribute) Storage (class in lamindb) storage (lamindb.Artifact attribute) (lamindb.core.Settings attribute) (lamindb.setup.core.InstanceSettings attribute) (lamindb.setup.core.SetupSettings attribute) storage_local (lamindb.core.Settings attribute) (lamindb.setup.core.InstanceSettings attribute) storage_options (lamindb.UPath attribute) storage_set (lamindb.Run attribute) (lamindb.User attribute) StorageSettings (class in lamindb.setup.core) StrField (in module lamindb.core.types) strip() (lamindb.core.types.TransformType method) suffix (lamindb.Artifact attribute) (lamindb.UPath attribute) suffixes (lamindb.UPath attribute) swapcase() (lamindb.core.types.TransformType method) symbol (bionty.Gene attribute) symlink_to() (lamindb.UPath method) sync_all_public_sources_to_latest() (in module bionty.core) sync_git_repo (lamindb.core.Settings attribute) synchronize() (lamindb.UPath method) synonyms (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.Pathway attribute) (bionty.Phenotype attribute) (bionty.Protein attribute) (bionty.Tissue attribute) (lamindb.Feature attribute) synonyms_mapper (lamindb.core.InspectResult attribute) system (wetlab.Treatment attribute) T targets (wetlab.Treatment attribute) Techsample (class in wetlab) Tissue (class in bionty) tissue_set (lamindb.Run attribute) (lamindb.User attribute) tissues (wetlab.Biosample attribute) title() (lamindb.core.types.TransformType method) to_pronto() (bionty.core.PublicOntology method) to_url() (lamindb.UPath method) torch_worker_init_fn() (lamindb.core.MappedCollection static method) touch() (lamindb.UPath method) track() (in module lamindb) track_run_inputs (lamindb.core.Settings attribute) TracksRun (class in lamindb.core) TracksUpdates (class in lamindb.core) Transform (class in lamindb) transform (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.core.run_context attribute) (lamindb.core.Settings attribute) (lamindb.Run attribute) transform_set (lamindb.User attribute) TransformSettings (class in lamindb.core) TransformType (class in lamindb.core.types) translate() (lamindb.core.types.TransformType method) Treatment (class in wetlab) TreatmentTarget (class in wetlab) type (lamindb.Artifact attribute) (lamindb.setup.core.StorageSettings attribute) (lamindb.Storage attribute) (lamindb.Transform attribute) (wetlab.Treatment attribute) type_is_cloud (lamindb.setup.core.StorageSettings attribute) U uid (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.PublicSource attribute) (bionty.Tissue attribute) (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.Feature attribute) (lamindb.FeatureSet attribute) (lamindb.Run attribute) (lamindb.setup.core.InstanceSettings attribute) (lamindb.setup.core.StorageSettings attribute) (lamindb.setup.core.UserSettings attribute) (lamindb.Storage attribute) (lamindb.Transform attribute) (lamindb.ULabel attribute) (lamindb.User attribute) (wetlab.Biosample attribute) (wetlab.Experiment attribute) (wetlab.ExperimentType attribute) (wetlab.Techsample attribute) (wetlab.Treatment attribute) (wetlab.TreatmentTarget attribute) (wetlab.Well attribute) ULabel (class in lamindb) ulabel_set (lamindb.Run attribute) (lamindb.User attribute) ulabels (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.Transform attribute) uniprotkb_id (bionty.CellMarker attribute) (bionty.Protein attribute) unit (lamindb.Feature attribute) unlink() (lamindb.UPath method) unordered_artifacts (lamindb.Collection attribute) UPath (class in lamindb) UPathStr (in module lamindb.core.types) 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.PublicSource attribute) (bionty.Tissue attribute) (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.core.TracksUpdates attribute) (lamindb.Feature attribute) (lamindb.Param attribute) (lamindb.Storage attribute) (lamindb.Transform attribute) (lamindb.ULabel attribute) (lamindb.User attribute) (wetlab.Biosample attribute) (wetlab.Experiment attribute) (wetlab.ExperimentType attribute) (wetlab.Techsample attribute) (wetlab.Treatment attribute) (wetlab.TreatmentTarget attribute) (wetlab.Well attribute) UpdateTransformSettings upload (lamindb.core.types.TransformType attribute) upload_from() (lamindb.UPath method) upon_artifact_create_if_hash_exists (lamindb.core.Settings attribute) upon_create_search_names (lamindb.core.Settings attribute) upon_file_create_skip_size_hash (lamindb.core.Settings attribute) upper() (lamindb.core.types.TransformType method) url (bionty.PublicSource attribute) use_in_migrations (lamindb.core.QueryManager attribute) User (class in lamindb) user (lamindb.setup.core.SetupSettings attribute) UserSettings (class in lamindb.setup.core) using() (lamindb.core.Registry class method) V validate() (bionty.core.PublicOntology method) (lamindb.core.AnnDataAnnotator method) (lamindb.core.CanValidate class method) (lamindb.core.DataFrameAnnotator method) (lamindb.core.MuDataAnnotator method) (lamindb.core.QuerySet method) validated (lamindb.core.InspectResult attribute) ValidationError value (lamindb.core.types.TransformType attribute) var_index (lamindb.core.AnnDataAnnotator attribute) (lamindb.core.MuDataAnnotator attribute) var_names (lamindb.core.storage.AnnDataAccessor attribute) verbosity (lamindb.core.Settings attribute) version (bionty.core.PublicOntology attribute) (bionty.PublicSource attribute) (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.core.IsVersioned attribute) (lamindb.core.TransformSettings attribute) (lamindb.Transform attribute) versions (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.core.IsVersioned attribute) (lamindb.Transform attribute) view() (in module lamindb) view_lineage() (lamindb.core.HasFeatures method) view_parents() (lamindb.core.HasParents method) view_tree() (lamindb.UPath method) visibility (lamindb.Artifact attribute) (lamindb.Collection attribute) W Well (class in wetlab) wetlab module with_segments() (lamindb.UPath method) Z zfill() (lamindb.core.types.TransformType method)