Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W A absolute() (lamindb.UPath method) access_token (lamindb.setup.core.UserSettings attribute) add() (lamindb.core.FeatureManager method) (lamindb.core.LabelManager method) add_from() (lamindb.core.LabelManager method) add_from_anndata() (lamindb.core.FeatureManager method) add_from_df() (lamindb.core.FeatureManager method) add_from_mudata() (lamindb.core.FeatureManager 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) 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.ValidationError attribute) Artifact (class in lamindb) artifact_use_virtual_keys (lamindb.core.Settings attribute) as_uri() (lamindb.UPath method) auto_created (lamindb.core.QueryManager attribute) auto_save_parents (bionty.core.Settings attribute) B backed() (lamindb.Artifact method) BackedAccessor (class in lamindb.core.storage) bionty module bionty.core module BioRegistry (class in bionty.core) C cache() (lamindb.Artifact method) (lamindb.Collection method) cache_dir (lamindb.setup.core.StorageSettings attribute) CanValidate (class in lamindb.core) categoricals (lamindb.core.AnnDataAnnotator attribute) (lamindb.core.MuDataAnnotator attribute) CellLine (class in bionty) CellMarker (class in bionty) CellType (class in bionty) check() (lamindb.setup.migrate class method) chmod() (lamindb.UPath 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) Collection (class in lamindb) connect() (in module lamindb) create() (lamindb.setup.migrate class method) creation_counter (lamindb.core.QueryManager attribute) cwd() (lamindb.UPath class method) D Data (class in lamindb.core) DataFrameAnnotator (class in lamindb.core) 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.Data method) DevelopmentalStage (class in bionty) 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) django() (in module lamindb.setup) download_to() (lamindb.UPath method) drive (lamindb.UPath attribute) E email (lamindb.setup.core.UserSettings attribute) Ethnicity (class in bionty) exists() (lamindb.UPath method) expanduser() (lamindb.UPath method) ExperimentalFactor (class in bionty) F fake_bio_notebook_titles() (in module lamindb.core.datasets) feature Feature (class in lamindb) FeatureManager (class in lamindb.core) features (lamindb.core.Data attribute) FeatureSet (class in lamindb) 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.Registry class method) finish() (in module lamindb) first() (lamindb.core.QuerySet 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) (lamindb.ULabel class method) fs (lamindb.UPath attribute) G Gene (class in bionty) 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_type_display() (lamindb.Transform method) git_repo (lamindb.setup.core.InstanceSettings attribute) glob() (lamindb.UPath method) group() (lamindb.UPath method) H handle (lamindb.setup.core.UserSettings attribute) hardlink_to() (lamindb.UPath method) HasParents (class in lamindb.core) home() (lamindb.UPath class method) I id (lamindb.setup.core.InstanceSettings attribute) (lamindb.setup.core.StorageSettings attribute) (lamindb.setup.core.UserSettings attribute) init() (in module lamindb.setup) inspect() (bionty.core.PublicOntology method) (lamindb.core.CanValidate class method) (lamindb.core.QuerySet method) InspectResult (class in lamindb.core) InstanceSettings (class in lamindb.setup.core) is_absolute() (lamindb.UPath method) is_block_device() (lamindb.UPath method) is_char_device() (lamindb.UPath method) is_dir() (lamindb.UPath method) is_fifo() (lamindb.UPath method) is_file() (lamindb.UPath method) is_mount() (lamindb.UPath method) is_remote (lamindb.setup.core.InstanceSettings attribute) is_socket() (lamindb.UPath method) is_symlink() (lamindb.UPath method) IsTree (class in lamindb.core) IsVersioned (class in lamindb.core) iterdir() (lamindb.UPath method) K key_to_filepath() (lamindb.setup.core.StorageSettings method) L label LabelManager (class in lamindb.core) labels (lamindb.core.Data 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_version() (lamindb.core.QuerySet method) lchmod() (lamindb.UPath method) link_to() (lamindb.UPath method) list() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) ListLike (in module lamindb.core.types) load() (lamindb.Artifact method) (lamindb.Collection method) local_filepath() (lamindb.setup.core.StorageSettings method) local_storage (lamindb.setup.core.InstanceSettings attribute) 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) lstat() (lamindb.UPath method) M map_synonyms() (bionty.core.PublicOntology method) (lamindb.core.CanValidate class method) mapped() (lamindb.Collection method) MappedCollection (class in lamindb.core) members (lamindb.FeatureSet attribute) migrate (class in lamindb.setup) 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 mudata_papalexi21_subset() (in module lamindb.core.datasets) MuDataAnnotator (class in lamindb.core) N n_empty (lamindb.core.InspectResult attribute) n_unique (lamindb.core.InspectResult attribute) name (lamindb.core.types.TransformType attribute) (lamindb.setup.core.InstanceSettings attribute) (lamindb.setup.core.UserSettings attribute) (lamindb.UPath attribute) non_validated (lamindb.core.InspectResult attribute) notebook (lamindb.core.types.TransformType attribute) O obs_names (lamindb.core.storage.AnnDataAccessor attribute) observation one() (lamindb.core.QuerySet method) (lamindb.core.RecordsList method) one_or_none() (lamindb.core.QuerySet method) open() (lamindb.UPath method) ordered (lamindb.core.QuerySet attribute) organism (bionty.core.PublicOntology attribute) (bionty.core.Settings attribute) Organism (class in bionty) original_shapes (lamindb.core.MappedCollection attribute) owner (lamindb.setup.core.InstanceSettings attribute) owner() (lamindb.UPath method) P parent (lamindb.UPath attribute) parents (lamindb.UPath attribute) parts (lamindb.UPath attribute) password (lamindb.setup.core.UserSettings attribute) path (lamindb.Artifact attribute) (lamindb.core.run_context attribute) (lamindb.UPath attribute) Pathway (class in bionty) Phenotype (class in bionty) pipeline (lamindb.core.types.TransformType attribute) Protein (class in bionty) protocol (lamindb.UPath attribute) public() (bionty.core.BioRegistry class method) PublicOntology (class in bionty.core) PublicSource (class in bionty) 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) region (lamindb.setup.core.StorageSettings attribute) register() (in module lamindb.setup) Registry (class in lamindb.core) relative_to() (lamindb.UPath method) remove_synonym() (lamindb.core.CanValidate method) rename() (lamindb.UPath method) replace() (lamindb.Artifact method) (lamindb.UPath method) resolve() (lamindb.UPath method) restore() (lamindb.Artifact method) (lamindb.Collection method) rglob() (lamindb.UPath method) rmdir() (lamindb.UPath method) root (lamindb.setup.core.StorageSettings attribute) (lamindb.UPath attribute) root_as_path() (lamindb.Storage method) root_as_str (lamindb.setup.core.StorageSettings attribute) Run (class in lamindb) run (lamindb.core.run_context attribute) run_context (class in lamindb.core) S samefile() (lamindb.UPath method) sample 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) script (lamindb.core.types.TransformType attribute) search() (bionty.core.PublicOntology method) (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) (lamindb.core.Registry class method) 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) shape (lamindb.core.MappedCollection attribute) show() (lamindb.setup.migrate class method) silence_file_run_transform_warning (lamindb.core.Settings attribute) slug (lamindb.setup.core.InstanceSettings attribute) source (bionty.core.PublicOntology attribute) squash() (lamindb.setup.migrate class method) stage() (lamindb.Artifact method) (lamindb.Collection method) standardize() (bionty.core.PublicOntology method) (lamindb.core.CanValidate class method) (lamindb.core.QuerySet method) stat() (lamindb.UPath method) stem (lamindb.UPath attribute) stem_uid (lamindb.core.IsVersioned attribute) Storage (class in lamindb) storage (lamindb.core.Settings attribute) (lamindb.setup.core.InstanceSettings attribute) storage_options (lamindb.UPath attribute) StorageSettings (class in lamindb.setup.core) StrField (in module lamindb.core.types) suffix (lamindb.UPath attribute) suffixes (lamindb.UPath 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_mapper (lamindb.core.InspectResult attribute) T Tissue (class in bionty) 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) Transform (class in lamindb) transform (lamindb.core.run_context attribute) (lamindb.core.Settings attribute) TransformType (class in lamindb.core.types) type (lamindb.setup.core.StorageSettings attribute) type_is_cloud (lamindb.setup.core.StorageSettings attribute) U uid (lamindb.setup.core.InstanceSettings attribute) (lamindb.setup.core.StorageSettings attribute) (lamindb.setup.core.UserSettings attribute) ULabel (class in lamindb) unlink() (lamindb.UPath method) UPath (class in lamindb) UPathStr (in module lamindb.core.types) 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) use_in_migrations (lamindb.core.QueryManager attribute) User (class in lamindb) 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) variable verbosity (lamindb.core.Settings attribute) version (bionty.core.PublicOntology attribute) versions (lamindb.core.IsVersioned attribute) view() (in module lamindb) view_lineage() (lamindb.core.Data method) view_parents() (lamindb.core.HasParents method) view_tree() (lamindb.Artifact class method) (lamindb.core.IsTree class method) (lamindb.core.QuerySet method) (lamindb.UPath method) W with_name() (lamindb.UPath method) with_suffix() (lamindb.UPath method)