Index

A

aaggregate() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) 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) (clinicore.Medication attribute) (ourprojects.Project attribute) (ourprojects.Reference attribute) (wetlab.Biologic attribute) (wetlab.Compound attribute) absolute() (lamindb.UPath method) abulk_create() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) abulk_update() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) access_token (lamindb.setup.core.UserSettings attribute) acontains() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) acount() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) acreate() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) add() (lamindb.core.LabelManager method) add_feature_set() (lamindb.core.FeatureManager method) add_from() (lamindb.core.LabelManager method) add_new_from() (lamindb.core.AnnDataCurator method) (lamindb.core.DataFrameCurator method) (lamindb.core.MuDataCurator method) (lamindb.core.SOMACurator method) add_new_from_columns() (lamindb.core.MuDataCurator method) add_new_from_var_index() (lamindb.core.AnnDataCurator method) (lamindb.core.MuDataCurator method) add_source() (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.Organism class method) (bionty.Pathway class method) (bionty.Phenotype class method) (bionty.Protein class method) (bionty.Tissue class method) (clinicore.Medication class method) (wetlab.Compound class method) add_synonym() (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.Organism method) (bionty.Pathway method) (bionty.Phenotype method) (bionty.Protein method) (bionty.Tissue method) (cellregistry.Cell method) (clinicore.Biosample method) (clinicore.ClinicalTrial method) (clinicore.Medication method) (clinicore.Patient method) (clinicore.Treatment method) (lamindb.core.CanCurate method) (lamindb.Feature method) (lamindb.Param method) (lamindb.ULabel method) (lamindb.User method) (ourprojects.Person method) (ourprojects.Project method) (ourprojects.Reference method) (wetlab.Biologic method) (wetlab.Biosample method) (wetlab.CombinationPerturbation method) (wetlab.Compound method) (wetlab.CompoundPerturbation method) (wetlab.Donor method) (wetlab.EnvironmentalPerturbation method) (wetlab.Experiment method) (wetlab.GeneticPerturbation method) (wetlab.PerturbationTarget method) (wetlab.Techsample method) (wetlab.Well method) add_values() (lamindb.core.FeatureManager method) (lamindb.core.ParamManager method) administered_datetime (clinicore.Treatment attribute) aearliest() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) aexists() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method)

aexplain() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) afirst() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) age (clinicore.Patient attribute) (wetlab.Donor attribute) aget() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) aget_or_create() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) aggregate() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) ain_bulk() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) aiterator() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) alast() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) alatest() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) alias() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) all() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) anchor (lamindb.UPath property) 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) AnnDataCurator (class in lamindb.core) annotate() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) api_key (lamindb.setup.core.UserSettings attribute) append() (lamindb.Collection method) (lamindb.core.RecordList method) args (lamindb.core.exceptions.DoesNotExist attribute) (lamindb.core.exceptions.IntegrityError attribute) (lamindb.core.exceptions.InvalidArgument attribute) (lamindb.core.exceptions.MissingContextUID attribute) (lamindb.core.exceptions.NotebookNotSaved attribute) (lamindb.core.exceptions.NoTitleError attribute) (lamindb.core.exceptions.RecordNameChangeIntegrityError attribute) (lamindb.core.exceptions.UpdateContext attribute) (lamindb.core.exceptions.ValidationError attribute) Artifact (class in lamindb) artifact_if_hash_exists (lamindb.core.subsettings.CreationSettings attribute) artifact_silence_missing_run_warning (lamindb.core.subsettings.CreationSettings attribute) artifact_skip_size_hash (lamindb.core.subsettings.CreationSettings 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.Source attribute) (bionty.Tissue attribute) (clinicore.Biosample attribute) (clinicore.ClinicalTrial attribute) (clinicore.Medication attribute) (clinicore.Patient attribute) (clinicore.Treatment attribute) (lamindb.Collection attribute) (lamindb.core.FeatureValue attribute) (lamindb.core.ParamValue attribute) (lamindb.FeatureSet attribute) (lamindb.Storage attribute) (lamindb.ULabel attribute) (ourprojects.Project attribute) (ourprojects.Reference attribute) (wetlab.Biologic attribute) (wetlab.Biosample attribute) (wetlab.CombinationPerturbation attribute) (wetlab.Compound attribute) (wetlab.CompoundPerturbation attribute) (wetlab.Donor attribute) (wetlab.EnvironmentalPerturbation attribute) (wetlab.Experiment attribute) (wetlab.GeneticPerturbation attribute) (wetlab.PerturbationTarget attribute) (wetlab.Techsample attribute) (wetlab.Well attribute) ArtifactType (in module lamindb.core.types) as_manager() (lamindb.core.QuerySet class method) as_posix() (lamindb.UPath method) as_uri() (lamindb.UPath method) aupdate() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) aupdate_or_create() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) authors (ourprojects.Reference attribute) auto_connect (lamindb.setup.core.SetupSettings property) auto_created (lamindb.core.QueryManager attribute)

B

BackedAccessor (class in lamindb.core.storage) BaseCurator (class in lamindb.core) batch (clinicore.Biosample attribute) (wetlab.Biosample attribute) (wetlab.Donor attribute) (wetlab.Techsample attribute) BFXPipeline (class in bionty.base) Biologic (class in wetlab) BiologicType (in module wetlab) bionty module bionty.base module

bionty.core module BioRecord (class in bionty.core) BioSample (class in bionty.base) Biosample (class in clinicore) (class in wetlab) biosamples (wetlab.Techsample attribute) biotype (bionty.Gene attribute) birth_date (clinicore.Patient attribute) bmi (wetlab.Donor attribute) bulk_create() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) bulk_update() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method)

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.core) categoricals (lamindb.core.AnnDataCurator property) (lamindb.core.MuDataCurator property) (lamindb.core.SOMACurator property) Cell (class in cellregistry) cell_lines (wetlab.Biosample attribute) cell_types (clinicore.Biosample attribute) (wetlab.Biosample attribute) CellLine (class in bionty) (class in bionty.base) CellMarker (class in bionty) (class in bionty.base) cellregistry module CellType (class in bionty) (class in bionty.base) check() (lamindb.core.QueryManager method) check_vars_non_aligned() (lamindb.core.MappedCollection method) check_vars_sorted() (lamindb.core.MappedCollection method) chembl_id (clinicore.Medication attribute) (wetlab.Compound attribute) children (lamindb.Run attribute) (lamindb.ULabel attribute) chmod() (lamindb.UPath method) clean_up_failed_runs() (lamindb.core.AnnDataCurator method) (lamindb.core.DataFrameCurator method) clear() (lamindb.core.RecordList method) clinical_trial (clinicore.Biosample attribute) ClinicalTrial (class in clinicore) clinicore module close() (in module lamindb.setup) (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) code (lamindb.core.exceptions.DoesNotExist attribute) (lamindb.core.exceptions.InvalidArgument attribute) (lamindb.core.exceptions.MissingContextUID attribute) (lamindb.core.exceptions.NotebookNotSaved attribute) (lamindb.core.exceptions.NoTitleError attribute) (lamindb.core.exceptions.RecordNameChangeIntegrityError attribute) (lamindb.core.exceptions.UpdateContext attribute) (lamindb.core.exceptions.ValidationError attribute) Collection (class in lamindb) collections (clinicore.ClinicalTrial attribute) (lamindb.Artifact attribute) (lamindb.ULabel attribute) column (wetlab.Well attribute) CombinationPerturbation (class in wetlab) complex_filter() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) COMPOSITE (lamindb.core.storage.VALID_SUFFIXES attribute) Compound (class in wetlab) compound (wetlab.CompoundPerturbation attribute) compound_perturbations (wetlab.CombinationPerturbation attribute) CompoundPerturbation (class in wetlab) concentration (wetlab.CompoundPerturbation attribute) concentration_unit (wetlab.CompoundPerturbation attribute) connect() (in module lamindb) contains() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) Context (class in lamindb.core) context (in module lamindb) contribute_to_class() (lamindb.core.QueryManager method) contributors (ourprojects.Project attribute) copy() (lamindb.core.RecordList method) count() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) (lamindb.core.RecordList method) create() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) (lamindb.setup.migrate class method) create_relationship() (bionty.base.Ontology method) create_term() (bionty.base.Ontology method) 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) (cellregistry.Cell attribute) (clinicore.Biosample attribute) (clinicore.ClinicalTrial attribute) (clinicore.Medication attribute) (clinicore.Patient attribute) (clinicore.Treatment attribute) (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.core.FeatureValue attribute) (lamindb.core.ParamValue 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) (ourprojects.Person attribute) (ourprojects.Project attribute) (ourprojects.Reference attribute) (wetlab.Biologic attribute) (wetlab.Biosample attribute) (wetlab.CombinationPerturbation attribute) (wetlab.Compound attribute) (wetlab.CompoundPerturbation attribute) (wetlab.Donor attribute) (wetlab.EnvironmentalPerturbation attribute) (wetlab.Experiment attribute) (wetlab.GeneticPerturbation attribute) (wetlab.PerturbationTarget attribute) (wetlab.Techsample 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.Source attribute) (bionty.Tissue attribute) (cellregistry.Cell attribute) (clinicore.Biosample attribute) (clinicore.ClinicalTrial attribute) (clinicore.Medication attribute) (clinicore.Patient attribute) (clinicore.Treatment attribute) (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.core.FeatureValue attribute) (lamindb.core.ParamValue 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) (ourprojects.Person attribute) (ourprojects.Project attribute) (ourprojects.Reference attribute) (wetlab.Biologic attribute) (wetlab.Biosample attribute) (wetlab.CombinationPerturbation attribute) (wetlab.Compound attribute) (wetlab.CompoundPerturbation attribute) (wetlab.Donor attribute) (wetlab.EnvironmentalPerturbation attribute) (wetlab.Experiment attribute) (wetlab.GeneticPerturbation attribute) (wetlab.PerturbationTarget attribute) (wetlab.Techsample attribute) (wetlab.Well attribute) created_by_id (lamindb.core.TracksRun attribute) created_runs (lamindb.User attribute) created_transforms (lamindb.User attribute) creation (lamindb.core.Settings property) creation_counter (lamindb.core.QueryManager attribute) CreationSettings (class in lamindb.core.subsettings) CurateLookup (class in lamindb.core) Curator (class in lamindb) currently_used (bionty.Source attribute) cwd() (lamindb.UPath class method)

D

data_artifact (lamindb.Collection property) dataframe_artifact (bionty.Source attribute) DataFrameCurator (class in lamindb.core) date (wetlab.Experiment attribute) dates() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) datetimes() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) db (lamindb.core.QueryManager property) (lamindb.core.QuerySet property) (lamindb.setup.core.InstanceSettings property) db_manager() (lamindb.core.QueryManager method) deceased (clinicore.Patient attribute) deceased_date (clinicore.Patient attribute) deconstruct() (lamindb.core.QueryManager method) defer() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) defined_migrations() (lamindb.setup.migrate class method) delete() (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.Organism method) (bionty.Pathway method) (bionty.Phenotype method) (bionty.Protein method) (bionty.Source method) (bionty.Tissue method) (cellregistry.Cell method) (clinicore.Biosample method) (clinicore.ClinicalTrial method) (clinicore.Medication method) (clinicore.Patient method) (clinicore.Treatment method) (in module lamindb.setup) (lamindb.Artifact method) (lamindb.Collection method) (lamindb.core.FeatureValue method) (lamindb.core.IsVersioned method) (lamindb.core.ParamValue method) (lamindb.core.QuerySet method) (lamindb.core.Record method) (lamindb.core.TracksRun method) (lamindb.core.TracksUpdates method) (lamindb.Feature method) (lamindb.FeatureSet method) (lamindb.Param method) (lamindb.Run method) (lamindb.Storage method) (lamindb.Transform method) (lamindb.ULabel method) (lamindb.User method) (ourprojects.Person method) (ourprojects.Project method) (ourprojects.Reference method) (wetlab.Biologic method) (wetlab.Biosample method) (wetlab.CombinationPerturbation method) (wetlab.Compound method) (wetlab.CompoundPerturbation method) (wetlab.Donor method) (wetlab.EnvironmentalPerturbation method) (wetlab.Experiment method) (wetlab.GeneticPerturbation method) (wetlab.PerturbationTarget method) (wetlab.Techsample method) (wetlab.Well method) deploy() (lamindb.setup.migrate class method) deployed_migrations() (lamindb.setup.migrate class method) describe() (lamindb.Artifact method) (lamindb.Collection method) description (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) (cellregistry.Cell attribute) (clinicore.Biosample attribute) (clinicore.ClinicalTrial attribute) (clinicore.Medication attribute) (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.Feature attribute) (lamindb.Storage attribute) (lamindb.Transform attribute) (lamindb.ULabel attribute) (ourprojects.Reference attribute) (wetlab.Biologic attribute) (wetlab.Biosample attribute) (wetlab.CombinationPerturbation attribute) (wetlab.Compound attribute) (wetlab.CompoundPerturbation attribute) (wetlab.Donor attribute) (wetlab.EnvironmentalPerturbation attribute) (wetlab.Experiment attribute) (wetlab.GeneticPerturbation attribute) (wetlab.PerturbationTarget attribute) (wetlab.Techsample attribute) DevelopmentalStage (class in bionty) (class in bionty.base) df (lamindb.core.InspectResult property) df() (bionty.base.BFXPipeline method) (bionty.base.BioSample method) (bionty.base.CellLine method) (bionty.base.CellMarker method) (bionty.base.CellType method) (bionty.base.DevelopmentalStage method) (bionty.base.Disease method) (bionty.base.Drug method) (bionty.base.Ethnicity method) (bionty.base.ExperimentalFactor method) (bionty.base.Gene method) (bionty.base.Organism method) (bionty.base.Pathway method) (bionty.base.Phenotype method) (bionty.base.Protein method) (bionty.base.PublicOntology method) (bionty.base.Tissue method) (bionty.CellLine class method) (bionty.CellMarker class method) (bionty.CellType class method) (bionty.core.BioRecord class method) (bionty.core.StaticReference 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) (cellregistry.Cell class method) (clinicore.Biosample class method) (clinicore.ClinicalTrial class method) (clinicore.Medication class method) (clinicore.Patient class method) (clinicore.Treatment class method) (lamindb.Artifact class method) (lamindb.Collection class method) (lamindb.core.FeatureValue class method) (lamindb.core.ParamValue class method) (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) (lamindb.core.Record class method) (lamindb.core.RecordList method) (lamindb.core.Registry method) (lamindb.Feature class method) (lamindb.FeatureSet class method) (lamindb.Param class method) (lamindb.Run class method) (lamindb.Storage class method) (lamindb.Transform class method) (lamindb.ULabel class method) (lamindb.User class method) (ourprojects.Person class method) (ourprojects.Project class method) (ourprojects.Reference class method) (wetlab.Biologic class method) (wetlab.Biosample class method) (wetlab.CombinationPerturbation class method) (wetlab.Compound class method) (wetlab.CompoundPerturbation class method) (wetlab.Donor class method) (wetlab.EnvironmentalPerturbation class method) (wetlab.Experiment class method) (wetlab.GeneticPerturbation class method) (wetlab.PerturbationTarget class method) (wetlab.Techsample class method) (wetlab.Well 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 property) diff() (bionty.base.BFXPipeline method) (bionty.base.BioSample method) (bionty.base.CellLine method) (bionty.base.CellMarker method) (bionty.base.CellType method) (bionty.base.DevelopmentalStage method) (bionty.base.Disease method) (bionty.base.Drug method) (bionty.base.Ethnicity method) (bionty.base.ExperimentalFactor method) (bionty.base.Gene method) (bionty.base.Organism method) (bionty.base.Pathway method) (bionty.base.Phenotype method) (bionty.base.Protein method) (bionty.base.PublicOntology method) (bionty.base.Tissue method) (bionty.core.StaticReference method) difference() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) dir_iris_images() (in module lamindb.core.datasets) dir_scrnaseq_cellranger() (in module lamindb.core.datasets) Disease (class in bionty) (class in bionty.base) diseases (clinicore.Biosample attribute) (wetlab.Biosample attribute) (wetlab.Donor attribute) display_available_sources() (in module bionty.base) display_currently_used_sources() (in module bionty.base) distinct() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) django() (in module lamindb.setup) DoesNotExist doi (ourprojects.Reference attribute) Donor (class in wetlab) dosage (clinicore.Treatment attribute) dosage_unit (clinicore.Treatment attribute) download_to() (lamindb.UPath method) drive (lamindb.UPath property) Drug (class in bionty.base) dtype (lamindb.Feature attribute) (lamindb.FeatureSet attribute) (lamindb.Param attribute) dump() (bionty.base.Ontology method) dumps() (bionty.base.Ontology method) duration (clinicore.Treatment attribute) (wetlab.CompoundPerturbation attribute) (wetlab.EnvironmentalPerturbation attribute)

E

earliest() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) email (lamindb.setup.core.UserSettings attribute) (ourprojects.Person attribute) ensembl_gene_id (bionty.Gene attribute) ensembl_gene_ids (bionty.Protein attribute) entity (bionty.Source attribute) environment (lamindb.Run attribute) environmental_perturbations (wetlab.CombinationPerturbation attribute) EnvironmentalPerturbation (class in wetlab) Ethnicity (class in bionty) (class in bionty.base) ethnicity (clinicore.Patient attribute) (wetlab.Donor attribute)

exclude() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) exists() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) (lamindb.UPath method) expanduser() (lamindb.UPath method) Experiment (class in wetlab) ExperimentalFactor (class in bionty) (class in bionty.base) explain() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) extend() (lamindb.core.RecordList method) external (ourprojects.Person attribute) extra() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method)

F

FAIR fake_bio_notebook_titles() (in module lamindb.core.datasets) feature Feature (class in lamindb) feature (lamindb.core.FeatureValue attribute) feature_sets (bionty.CellMarker attribute) (bionty.Gene attribute) (bionty.Pathway attribute) (bionty.Protein attribute) (lamindb.Artifact attribute) (lamindb.Feature attribute) FeatureDtype (in module lamindb.core.types) FeatureManager (class in lamindb.core) features (lamindb.Artifact attribute) (lamindb.FeatureSet attribute) FeatureSet (class in lamindb) FeatureValue (class in lamindb.core) FieldAttr (in module lamindb.core.fields) fields (bionty.base.BFXPipeline property) (bionty.base.BioSample property) (bionty.base.CellLine property) (bionty.base.CellMarker property) (bionty.base.CellType property) (bionty.base.DevelopmentalStage property) (bionty.base.Disease property) (bionty.base.Drug property) (bionty.base.Ethnicity property) (bionty.base.ExperimentalFactor property) (bionty.base.Gene property) (bionty.base.Organism property) (bionty.base.Pathway property) (bionty.base.Phenotype property) (bionty.base.Protein property) (bionty.base.PublicOntology property) (bionty.base.Tissue property) (bionty.core.StaticReference property) (lamindb.core.AnnDataCurator property) (lamindb.core.DataFrameCurator property) 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() (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.Organism class method) (bionty.Pathway class method) (bionty.Phenotype class method) (bionty.Protein class method) (bionty.Source class method) (bionty.Tissue class method) (cellregistry.Cell class method) (clinicore.Biosample class method) (clinicore.ClinicalTrial class method) (clinicore.Medication class method) (clinicore.Patient class method) (clinicore.Treatment class method) (lamindb.Artifact class method) (lamindb.Collection class method) (lamindb.core.FeatureManager class method) (lamindb.core.FeatureValue class method) (lamindb.core.ParamManager class method) (lamindb.core.ParamValue class method) (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) (lamindb.core.Record class method) (lamindb.core.Registry method) (lamindb.Feature class method) (lamindb.FeatureSet class method) (lamindb.Param class method) (lamindb.Run class method) (lamindb.Storage class method) (lamindb.Transform class method) (lamindb.ULabel class method) (lamindb.User class method) (ourprojects.Person class method) (ourprojects.Project class method) (ourprojects.Reference class method) (wetlab.Biologic class method) (wetlab.Biosample class method) (wetlab.CombinationPerturbation class method) (wetlab.Compound class method) (wetlab.CompoundPerturbation class method) (wetlab.Donor class method) (wetlab.EnvironmentalPerturbation class method) (wetlab.Experiment class method) (wetlab.GeneticPerturbation class method) (wetlab.PerturbationTarget class method) (wetlab.Techsample class method) (wetlab.Well class method)

finish() (in module lamindb) (lamindb.core.Context method) finished_at (lamindb.Run attribute) first() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) frac_validated (lamindb.core.InspectResult property) from_anndata() (lamindb.Artifact class method) (lamindb.Curator class method) from_df() (lamindb.Artifact class method) (lamindb.Curator class method) (lamindb.Feature class method) (lamindb.FeatureSet class method) from_dir() (lamindb.Artifact class method) from_mudata() (lamindb.Artifact class method) (lamindb.Curator class method) from_obo_library() (bionty.base.Ontology class method) from_queryset() (lamindb.core.QueryManager class method) from_source() (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.Organism class method) (bionty.Pathway class method) (bionty.Phenotype class method) (bionty.Protein class method) (bionty.Tissue class method) (clinicore.Medication class method) (wetlab.Compound class method) from_spatialdata() (lamindb.Curator class method) from_tiledbsoma() (lamindb.Curator class method) from_values() (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.Organism class method) (bionty.Pathway class method) (bionty.Phenotype class method) (bionty.Protein class method) (bionty.Tissue class method) (cellregistry.Cell class method) (clinicore.Biosample class method) (clinicore.ClinicalTrial class method) (clinicore.Medication class method) (clinicore.Patient class method) (clinicore.Treatment class method) (lamindb.core.CanCurate class method) (lamindb.Feature class method) (lamindb.FeatureSet class method) (lamindb.Param class method) (lamindb.ULabel class method) (lamindb.User class method) (ourprojects.Person class method) (ourprojects.Project class method) (ourprojects.Reference class method) (wetlab.Biologic class method) (wetlab.Biosample class method) (wetlab.CombinationPerturbation class method) (wetlab.Compound class method) (wetlab.CompoundPerturbation class method) (wetlab.Donor class method) (wetlab.EnvironmentalPerturbation class method) (wetlab.Experiment class method) (wetlab.GeneticPerturbation class method) (wetlab.PerturbationTarget class method) (wetlab.Techsample class method) (wetlab.Well class method) fs (lamindb.UPath property)

G

gender (clinicore.Patient attribute) GENDER_CHOICES (clinicore.Patient attribute) Gene (class in bionty) (class in bionty.base) gene_symbol (bionty.CellMarker attribute) (bionty.Protein attribute) genes (bionty.Pathway attribute) (wetlab.PerturbationTarget attribute) genetic_perturbations (wetlab.CombinationPerturbation attribute) GeneticPerturbation (class in wetlab) GeneticPerturbationSystem (in module wetlab) get() (bionty.base.Ontology method) (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.Organism class method) (bionty.Pathway class method) (bionty.Phenotype class method) (bionty.Protein class method) (bionty.Source class method) (bionty.Tissue class method) (cellregistry.Cell class method) (clinicore.Biosample class method) (clinicore.ClinicalTrial class method) (clinicore.Medication class method) (clinicore.Patient class method) (clinicore.Treatment class method) (lamindb.Artifact class method) (lamindb.Collection class method) (lamindb.core.FeatureManager class method) (lamindb.core.FeatureValue class method) (lamindb.core.LabelManager method) (lamindb.core.ParamValue class method) (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) (lamindb.core.Record class method) (lamindb.core.Registry method) (lamindb.Feature class method) (lamindb.FeatureSet class method) (lamindb.Param class method) (lamindb.Run class method) (lamindb.Storage class method) (lamindb.Transform class method) (lamindb.ULabel class method) (lamindb.User class method) (ourprojects.Person class method) (ourprojects.Project class method) (ourprojects.Reference class method) (wetlab.Biologic class method) (wetlab.Biosample class method) (wetlab.CombinationPerturbation class method) (wetlab.Compound class method) (wetlab.CompoundPerturbation class method) (wetlab.Donor class method) (wetlab.EnvironmentalPerturbation class method) (wetlab.Experiment class method) (wetlab.GeneticPerturbation class method) (wetlab.PerturbationTarget class method) (wetlab.Techsample class method) (wetlab.Well class method)

get_gender_display() (clinicore.Patient method) 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.core.QueryManager method) (lamindb.core.QuerySet method) get_queryset() (lamindb.core.QueryManager method) get_relationship() (bionty.base.Ontology method) get_status_display() (clinicore.Treatment method) get_synonym_type() (bionty.base.Ontology method) get_term() (bionty.base.Ontology method) get_values() (lamindb.core.FeatureManager method) (lamindb.core.ParamManager method) git_repo (lamindb.setup.core.InstanceSettings property) glob() (lamindb.UPath method) group() (lamindb.UPath method) GUI

H

handle (lamindb.setup.core.UserSettings attribute) (lamindb.User attribute) hardlink_to() (lamindb.UPath method) hash (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.FeatureSet attribute) (lamindb.Transform attribute)

HasParents (class in lamindb.core) home() (lamindb.UPath class method)

I

id (lamindb.setup.core.StorageSettings property) (lamindb.setup.core.UserSettings property) import_source() (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.Organism class method) (bionty.Pathway class method) (bionty.Phenotype class method) (bionty.Protein class method) (bionty.Tissue class method) (clinicore.Medication class method) (wetlab.Compound class method) in_bulk() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) in_db (bionty.Source attribute) index() (lamindb.core.RecordList method) init() (in module lamindb.setup) input_artifacts (lamindb.Run attribute) input_collections (lamindb.Run attribute) input_of_runs (lamindb.Artifact attribute) (lamindb.Collection attribute) insert() (lamindb.core.RecordList method) inspect() (bionty.base.BFXPipeline method) (bionty.base.BioSample method) (bionty.base.CellLine method) (bionty.base.CellMarker method) (bionty.base.CellType method) (bionty.base.DevelopmentalStage method) (bionty.base.Disease method) (bionty.base.Drug method) (bionty.base.Ethnicity method) (bionty.base.ExperimentalFactor method) (bionty.base.Gene method) (bionty.base.Organism method) (bionty.base.Pathway method) (bionty.base.Phenotype method) (bionty.base.Protein method) (bionty.base.PublicOntology method) (bionty.base.Tissue method) (bionty.CellLine class method) (bionty.CellMarker class method) (bionty.CellType class method) (bionty.core.BioRecord class method) (bionty.core.StaticReference 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) (cellregistry.Cell class method) (clinicore.Biosample class method) (clinicore.ClinicalTrial class method) (clinicore.Medication class method) (clinicore.Patient class method) (clinicore.Treatment class method) (lamindb.core.CanCurate class method) (lamindb.core.QuerySet method) (lamindb.Feature class method) (lamindb.Param class method) (lamindb.ULabel class method) (lamindb.User class method) (ourprojects.Person class method) (ourprojects.Project class method) (ourprojects.Reference class method) (wetlab.Biologic class method) (wetlab.Biosample class method) (wetlab.CombinationPerturbation class method) (wetlab.Compound class method) (wetlab.CompoundPerturbation class method) (wetlab.Donor class method) (wetlab.EnvironmentalPerturbation class method) (wetlab.Experiment class method) (wetlab.GeneticPerturbation class method) (wetlab.PerturbationTarget class method) (wetlab.Techsample class method) (wetlab.Well class method)

InspectResult (class in lamindb.core) instance (lamindb.setup.core.SetupSettings property) instance_uid (lamindb.Storage attribute) InstanceSettings (class in lamindb.setup.core) instrument (bionty.ExperimentalFactor attribute) IntegrityError intersection() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) InvalidArgument is_absolute() (lamindb.UPath method) 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_latest (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.Transform attribute) is_mount() (lamindb.UPath method) is_on_hub (lamindb.setup.core.InstanceSettings property) (lamindb.setup.core.StorageSettings property) is_relative_to() (lamindb.UPath method) is_remote (lamindb.setup.core.InstanceSettings property) is_reserved() (lamindb.UPath method) is_socket() (lamindb.UPath method) is_symlink() (lamindb.UPath method) IsVersioned (class in lamindb.core) items() (bionty.base.Ontology method) iterator() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) iterdir() (lamindb.UPath method)

J

joinpath() (lamindb.UPath method)

joinuri() (lamindb.UPath method) journal (ourprojects.Reference attribute)

K

keep_artifacts_local (lamindb.setup.core.InstanceSettings property) key (lamindb.Artifact attribute) (lamindb.Transform attribute)

key_to_filepath() (lamindb.setup.core.StorageSettings method) keys() (bionty.base.Ontology method)

L

label LabelManager (class in lamindb.core) labels (lamindb.Artifact property) lakehouse lamindb module lamindb.core module lamindb.core.datasets module lamindb.core.exceptions module lamindb.core.fields module lamindb.core.loaders module lamindb.core.storage module lamindb.core.subsettings module lamindb.core.types module lamindb.integrations module lamindb.setup module lamindb.setup.core module last() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) latest() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) latest_run (lamindb.Transform property) latest_version() (lamindb.core.QuerySet method) lchmod() (lamindb.UPath method) length (bionty.Protein attribute) list() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) ListLike (in module lamindb.core.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) logger (in module lamindb.core) login() (in module lamindb.setup) logout() (in module lamindb.setup) lookup() (bionty.base.BFXPipeline method) (bionty.base.BioSample method) (bionty.base.CellLine method) (bionty.base.CellMarker method) (bionty.base.CellType method) (bionty.base.DevelopmentalStage method) (bionty.base.Disease method) (bionty.base.Drug method) (bionty.base.Ethnicity method) (bionty.base.ExperimentalFactor method) (bionty.base.Gene method) (bionty.base.Organism method) (bionty.base.Pathway method) (bionty.base.Phenotype method) (bionty.base.Protein method) (bionty.base.PublicOntology method) (bionty.base.Tissue method) (bionty.CellLine class method) (bionty.CellMarker class method) (bionty.CellType class method) (bionty.core.BioRecord class method) (bionty.core.StaticReference 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) (cellregistry.Cell class method) (clinicore.Biosample class method) (clinicore.ClinicalTrial class method) (clinicore.Medication class method) (clinicore.Patient class method) (clinicore.Treatment class method) (lamindb.Artifact class method) (lamindb.Collection class method) (lamindb.core.AnnDataCurator method) (lamindb.core.DataFrameCurator method) (lamindb.core.FeatureValue class method) (lamindb.core.MuDataCurator method) (lamindb.core.ParamValue class method) (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) (lamindb.core.Record class method) (lamindb.core.Registry method) (lamindb.core.SOMACurator method) (lamindb.Feature class method) (lamindb.FeatureSet class method) (lamindb.Param class method) (lamindb.Run class method) (lamindb.Storage class method) (lamindb.Transform class method) (lamindb.ULabel class method) (lamindb.User class method) (ourprojects.Person class method) (ourprojects.Project class method) (ourprojects.Reference class method) (wetlab.Biologic class method) (wetlab.Biosample class method) (wetlab.CombinationPerturbation class method) (wetlab.Compound class method) (wetlab.CompoundPerturbation class method) (wetlab.Donor class method) (wetlab.EnvironmentalPerturbation class method) (wetlab.Experiment class method) (wetlab.GeneticPerturbation class method) (wetlab.PerturbationTarget class method) (wetlab.Techsample class method) (wetlab.Well class method)

lstat() (lamindb.UPath method)

M

make_external() (lamindb.core.FeatureManager method) (lamindb.core.LabelManager method) map_legacy_ids() (bionty.base.Gene method) map_synonyms() (bionty.base.BFXPipeline method) (bionty.base.BioSample method) (bionty.base.CellLine method) (bionty.base.CellMarker method) (bionty.base.CellType method) (bionty.base.DevelopmentalStage method) (bionty.base.Disease method) (bionty.base.Drug method) (bionty.base.Ethnicity method) (bionty.base.ExperimentalFactor method) (bionty.base.Gene method) (bionty.base.Organism method) (bionty.base.Pathway method) (bionty.base.Phenotype method) (bionty.base.Protein method) (bionty.base.PublicOntology method) (bionty.base.Tissue method) (bionty.core.StaticReference method) mapped() (lamindb.Collection method) MappedCollection (class in lamindb.core) match() (lamindb.UPath method) md5 (bionty.Source attribute) measurement (bionty.ExperimentalFactor attribute) Medication (class in clinicore) medication (clinicore.Treatment attribute) medications (clinicore.Biosample attribute) members (lamindb.FeatureSet property) (wetlab.CombinationPerturbation property)

Meta (lamindb.core.IsVersioned attribute) (lamindb.core.TracksRun attribute) (lamindb.core.TracksUpdates attribute) meta_artifact (lamindb.Collection attribute) migrate (class in lamindb.setup) MissingContextUID mkdir() (lamindb.UPath method) modified (lamindb.UPath property) module bionty bionty.base bionty.core cellregistry clinicore lamindb lamindb.core lamindb.core.datasets lamindb.core.exceptions lamindb.core.fields lamindb.core.loaders lamindb.core.storage lamindb.core.subsettings lamindb.core.types lamindb.integrations lamindb.setup lamindb.setup.core ourprojects wetlab molecule (bionty.ExperimentalFactor attribute) mudata_papalexi21_subset() (in module lamindb.core.datasets) MuDataCurator (class in lamindb.core)

N

n (lamindb.FeatureSet attribute) n_empty (lamindb.core.InspectResult property) n_objects (lamindb.Artifact attribute) n_observations (lamindb.Artifact attribute) n_unique (lamindb.core.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) (cellregistry.Cell attribute) (clinicore.Biosample attribute) (clinicore.ClinicalTrial attribute) (clinicore.Medication attribute) (clinicore.Patient attribute) (clinicore.Treatment attribute) (lamindb.Collection attribute) (lamindb.core.Context property) (lamindb.core.subsettings.TransformSettings attribute) (lamindb.Feature attribute) (lamindb.FeatureSet attribute) (lamindb.Param attribute) (lamindb.setup.core.InstanceSettings property) (lamindb.setup.core.UserSettings attribute) (lamindb.Transform attribute) (lamindb.ULabel attribute) (lamindb.UPath property) (lamindb.User attribute) (ourprojects.Person attribute) (ourprojects.Project attribute) (ourprojects.Reference attribute) (wetlab.Biologic attribute) (wetlab.Biosample attribute) (wetlab.CombinationPerturbation attribute) (wetlab.Compound attribute) (wetlab.CompoundPerturbation attribute) (wetlab.Donor attribute) (wetlab.EnvironmentalPerturbation attribute) (wetlab.Experiment attribute) (wetlab.GeneticPerturbation attribute) (wetlab.PerturbationTarget attribute) (wetlab.Techsample attribute) (wetlab.Well attribute)

ncbi_gene_id (bionty.CellMarker attribute) ncbi_gene_ids (bionty.Gene attribute) non_validated (lamindb.core.AnnDataCurator property) (lamindb.core.DataFrameCurator property) (lamindb.core.InspectResult property) (lamindb.core.MuDataCurator property) (lamindb.core.SOMACurator property) none() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) NotebookNotSaved NoTitleError

O

objective (clinicore.ClinicalTrial attribute) obs_names (lamindb.core.storage.AnnDataAccessor property) observation off_target_score (wetlab.GeneticPerturbation attribute) on_target_score (wetlab.GeneticPerturbation attribute) one() (lamindb.core.QuerySet method) (lamindb.core.RecordList method) one_or_none() (lamindb.core.QuerySet method) only() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) Ontology (class in bionty.base) 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) (clinicore.Medication attribute) (wetlab.CombinationPerturbation attribute) (wetlab.Compound attribute) (wetlab.EnvironmentalPerturbation attribute) open() (lamindb.Artifact method) (lamindb.UPath method) order_by() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) ordered (lamindb.core.QuerySet property) ordered_artifacts (lamindb.Collection property) organism (bionty.base.BFXPipeline property) (bionty.base.BioSample property) (bionty.base.CellLine property) (bionty.base.CellMarker property) (bionty.base.CellType property) (bionty.base.DevelopmentalStage property) (bionty.base.Disease property) (bionty.base.Drug property) (bionty.base.Ethnicity property) (bionty.base.ExperimentalFactor property) (bionty.base.Gene property) (bionty.base.Organism property) (bionty.base.Pathway property) (bionty.base.Phenotype property) (bionty.base.Protein property) (bionty.base.PublicOntology property) (bionty.base.Tissue property) (bionty.CellMarker attribute) (bionty.core.Settings property) (bionty.core.StaticReference property) (bionty.Gene attribute) (bionty.Protein attribute) (bionty.Source attribute)

Organism (class in bionty) (class in bionty.base) organism (wetlab.Biosample attribute) (wetlab.Donor attribute) original_shapes (lamindb.core.MappedCollection property) ORM ourprojects module output_artifacts (lamindb.Run attribute) (lamindb.Transform attribute) output_collections (lamindb.Run attribute) (lamindb.Transform attribute) owner (lamindb.setup.core.InstanceSettings property) owner() (lamindb.UPath method)

P

Param (class in lamindb) param (lamindb.core.ParamValue attribute) ParamManager (class in lamindb.core) params (lamindb.Artifact attribute) (lamindb.Run attribute) ParamValue (class in lamindb.core) parent (lamindb.Run attribute) (lamindb.UPath property) 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) (clinicore.Medication attribute) (lamindb.ULabel attribute) (lamindb.UPath property) (wetlab.Compound attribute) parts (lamindb.UPath property) password (lamindb.setup.core.UserSettings attribute) path (lamindb.Artifact property) (lamindb.Storage property) (lamindb.UPath property) paths (lamindb.setup.core.SetupSettings property) Pathway (class in bionty) (class in bionty.base) pathways (wetlab.PerturbationTarget attribute) Patient (class in clinicore) patient (clinicore.Biosample attribute) Person (class in ourprojects) PerturbationTarget (class in wetlab) Phenotype (class in bionty) (class in bionty.base)

pk (lamindb.core.IsVersioned property) (lamindb.core.TracksRun property) (lamindb.core.TracksUpdates property) pop() (lamindb.core.RecordList method) predecessors (lamindb.Transform attribute) prefetch_related() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) preprint (ourprojects.Reference attribute) private_django_api (lamindb.setup.core.SetupSettings property) Project (class in ourprojects) Protein (class in bionty) (class in bionty.base) proteins (wetlab.Biologic attribute) (wetlab.PerturbationTarget attribute) protocol (lamindb.UPath property) public (ourprojects.Reference attribute) public() (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.Organism class method) (bionty.Pathway class method) (bionty.Phenotype class method) (bionty.Protein class method) (bionty.Tissue class method) (clinicore.Medication class method) (wetlab.Compound class method) PublicOntology (class in bionty.base) PublicOntologyField (class in bionty.base) published_at (ourprojects.Reference attribute) pubmed_id (ourprojects.Reference attribute)

Q

query (lamindb.core.QuerySet property) query_children() (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.Organism method) (bionty.Pathway method) (bionty.Phenotype method) (bionty.Protein method) (bionty.Tissue method) (clinicore.Medication method) (lamindb.core.HasParents method) (lamindb.ULabel method) (wetlab.Compound method)

query_parents() (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.Organism method) (bionty.Pathway method) (bionty.Phenotype method) (bionty.Protein method) (bionty.Tissue method) (clinicore.Medication method) (lamindb.core.HasParents method) (lamindb.ULabel method) (wetlab.Compound method) QueryManager (class in lamindb.core) QuerySet (class in lamindb.core)

R

raw() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) read_bytes() (lamindb.UPath method) read_text() (lamindb.UPath method) readlink() (lamindb.UPath method) record Record (class in lamindb.core) record (lamindb.setup.core.StorageSettings property) RecordList (class in lamindb.core) RecordNameChangeIntegrityError Reference (class in ourprojects) 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) references (ourprojects.Project attribute) region (lamindb.setup.core.StorageSettings property) (lamindb.Storage attribute) Registry (class in lamindb.core) registry (lamindb.FeatureSet attribute) relationships() (bionty.base.Ontology method) relative_to() (lamindb.UPath method) remove() (lamindb.core.RecordList method) remove_synonym() (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.Organism method) (bionty.Pathway method) (bionty.Phenotype method) (bionty.Protein method) (bionty.Tissue method) (cellregistry.Cell method) (clinicore.Biosample method) (clinicore.ClinicalTrial method) (clinicore.Medication method) (clinicore.Patient method) (clinicore.Treatment method) (lamindb.core.CanCurate method) (lamindb.Feature method) (lamindb.Param method) (lamindb.ULabel method) (lamindb.User method) (ourprojects.Person method) (ourprojects.Project method) (ourprojects.Reference method) (wetlab.Biologic method) (wetlab.Biosample method) (wetlab.CombinationPerturbation method) (wetlab.Compound method) (wetlab.CompoundPerturbation method) (wetlab.Donor method) (wetlab.EnvironmentalPerturbation method) (wetlab.Experiment method) (wetlab.GeneticPerturbation method) (wetlab.PerturbationTarget method) (wetlab.Techsample method) (wetlab.Well method) remove_values() (lamindb.core.FeatureManager method)

rename() (lamindb.UPath method) replace() (lamindb.Artifact method) (lamindb.UPath method) report (lamindb.Run attribute) reset_sources() (in module bionty.base) resolve() (lamindb.UPath method) resolve_expression() (lamindb.core.QuerySet method) restore() (lamindb.Artifact method) (lamindb.Collection method) reverse() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) (lamindb.core.RecordList 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) route (clinicore.Treatment attribute) row (wetlab.Well attribute) 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) (cellregistry.Cell attribute) Run (class in lamindb) run (clinicore.Biosample attribute) (clinicore.ClinicalTrial attribute) (clinicore.Medication attribute) (clinicore.Patient attribute) (clinicore.Treatment attribute) (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.core.Context property) (lamindb.core.FeatureValue attribute) (lamindb.core.TracksRun attribute) (lamindb.Feature attribute) (lamindb.FeatureSet attribute) (lamindb.Param attribute) (lamindb.Storage attribute) (lamindb.ULabel attribute) (ourprojects.Person attribute) (ourprojects.Project attribute) (ourprojects.Reference attribute) (wetlab.Biologic attribute) (wetlab.Biosample attribute) (wetlab.CombinationPerturbation attribute) (wetlab.Compound attribute) (wetlab.CompoundPerturbation attribute) (wetlab.Donor attribute) (wetlab.EnvironmentalPerturbation attribute) (wetlab.Experiment attribute) (wetlab.GeneticPerturbation attribute) (wetlab.PerturbationTarget attribute) (wetlab.Techsample attribute) (wetlab.Well attribute) run_id (lamindb.core.TracksRun attribute) runs (lamindb.core.ParamValue attribute) (lamindb.Transform attribute)

S

samefile() (lamindb.UPath method) sample 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.Organism method) (bionty.Pathway method) (bionty.Phenotype method) (bionty.Protein method) (bionty.Source method) (bionty.Tissue method) (cellregistry.Cell method) (clinicore.Biosample method) (clinicore.ClinicalTrial method) (clinicore.Medication method) (clinicore.Patient method) (clinicore.Treatment method) (in module lamindb) (lamindb.Artifact method) (lamindb.Collection method) (lamindb.core.FeatureValue method) (lamindb.core.IsVersioned method) (lamindb.core.ParamValue method) (lamindb.core.Record method) (lamindb.core.RecordList method) (lamindb.core.TracksRun method) (lamindb.core.TracksUpdates method) (lamindb.Feature method) (lamindb.FeatureSet method) (lamindb.Param method) (lamindb.Run method) (lamindb.Storage method) (lamindb.Transform method) (lamindb.ULabel method) (lamindb.User method) (ourprojects.Person method) (ourprojects.Project method) (ourprojects.Reference method) (wetlab.Biologic method) (wetlab.Biosample method) (wetlab.CombinationPerturbation method) (wetlab.Compound method) (wetlab.CompoundPerturbation method) (wetlab.Donor method) (wetlab.EnvironmentalPerturbation method) (wetlab.Experiment method) (wetlab.GeneticPerturbation method) (wetlab.PerturbationTarget method) (wetlab.Techsample method) (wetlab.Well method) save_artifact() (lamindb.core.AnnDataCurator method) (lamindb.core.BaseCurator method) (lamindb.core.DataFrameCurator method) (lamindb.core.MuDataCurator method) (lamindb.core.SOMACurator method) (lamindb.Curator method) save_tiledbsoma_experiment() (in module lamindb.integrations) save_vitessce_config() (in module lamindb.integrations) schema (lamindb.setup.core.InstanceSettings property) schmidt22_crispra_gws_IFNG() (in module lamindb.core.datasets) schmidt22_perturbseq() (in module lamindb.core.datasets) scientific_name (bionty.Organism attribute) search() (bionty.base.BFXPipeline method) (bionty.base.BioSample method) (bionty.base.CellLine method) (bionty.base.CellMarker method) (bionty.base.CellType method) (bionty.base.DevelopmentalStage method) (bionty.base.Disease method) (bionty.base.Drug method) (bionty.base.Ethnicity method) (bionty.base.ExperimentalFactor method) (bionty.base.Gene method) (bionty.base.Organism method) (bionty.base.Pathway method) (bionty.base.Phenotype method) (bionty.base.Protein method) (bionty.base.PublicOntology method) (bionty.base.Tissue method) (bionty.CellLine class method) (bionty.CellMarker class method) (bionty.CellType class method) (bionty.core.BioRecord class method) (bionty.core.StaticReference 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) (cellregistry.Cell class method) (clinicore.Biosample class method) (clinicore.ClinicalTrial class method) (clinicore.Medication class method) (clinicore.Patient class method) (clinicore.Treatment class method) (lamindb.Artifact class method) (lamindb.Collection class method) (lamindb.core.FeatureValue class method) (lamindb.core.ParamValue class method) (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) (lamindb.core.Record class method) (lamindb.core.Registry method) (lamindb.Feature class method) (lamindb.FeatureSet class method) (lamindb.Param class method) (lamindb.Run class method) (lamindb.Storage class method) (lamindb.Transform class method) (lamindb.ULabel class method) (lamindb.User class method) (ourprojects.Person class method) (ourprojects.Project class method) (ourprojects.Reference class method) (wetlab.Biologic class method) (wetlab.Biosample class method) (wetlab.CombinationPerturbation class method) (wetlab.Compound class method) (wetlab.CompoundPerturbation class method) (wetlab.Donor class method) (wetlab.EnvironmentalPerturbation class method) (wetlab.Experiment class method) (wetlab.GeneticPerturbation class method) (wetlab.PerturbationTarget class method) (wetlab.Techsample class method) (wetlab.Well class method) search_names (lamindb.core.subsettings.CreationSettings attribute) select_for_update() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) select_related() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) sequence (wetlab.GeneticPerturbation attribute) set_abbr() (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.Organism method) (bionty.Pathway method) (bionty.Phenotype method) (bionty.Protein method) (bionty.Tissue method) (cellregistry.Cell method) (clinicore.Biosample method) (clinicore.ClinicalTrial method) (clinicore.Medication method) (clinicore.Patient method) (clinicore.Treatment method) (lamindb.core.CanCurate method) (lamindb.Feature method) (lamindb.Param method) (lamindb.ULabel method) (lamindb.User method) (ourprojects.Person method) (ourprojects.Project method) (ourprojects.Reference method) (wetlab.Biologic method) (wetlab.Biosample method) (wetlab.CombinationPerturbation method) (wetlab.Compound method) (wetlab.CompoundPerturbation method) (wetlab.Donor method) (wetlab.EnvironmentalPerturbation method) (wetlab.Experiment method) (wetlab.GeneticPerturbation method) (wetlab.PerturbationTarget method) (wetlab.Techsample method) (wetlab.Well method)

set_as_currently_used() (bionty.Source method) set_latest_sources_as_currently_used() (in module bionty.core) 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) SetupSettings (class in lamindb.setup.core) sex (wetlab.Donor attribute) shape (lamindb.core.MappedCollection property) show() (lamindb.setup.migrate class method) SIMPLE (lamindb.core.storage.VALID_SUFFIXES attribute) site (clinicore.Treatment attribute) size (lamindb.Artifact attribute) slug (lamindb.setup.core.InstanceSettings property) small_dataset1() (in module lamindb.core.datasets) small_dataset2() (in module lamindb.core.datasets) SOMACurator (class in lamindb.core) sort() (lamindb.core.RecordList method) source (bionty.base.BFXPipeline property) (bionty.base.BioSample property) (bionty.base.CellLine property) (bionty.base.CellMarker property) (bionty.base.CellType property) (bionty.base.DevelopmentalStage property) (bionty.base.Disease property) (bionty.base.Drug property) (bionty.base.Ethnicity property) (bionty.base.ExperimentalFactor property) (bionty.base.Gene property) (bionty.base.Organism property) (bionty.base.Pathway property) (bionty.base.Phenotype property) (bionty.base.Protein property) (bionty.base.PublicOntology property) (bionty.base.Tissue property) (bionty.CellLine attribute) (bionty.CellMarker attribute) (bionty.CellType attribute) (bionty.core.BioRecord attribute) (bionty.core.StaticReference property) (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) Source (class in bionty) source (clinicore.Medication attribute) (wetlab.Compound attribute) source_code (lamindb.Transform attribute) source_website (bionty.Source attribute) squash() (lamindb.setup.migrate class method) stable_id (bionty.Gene attribute) standardize() (bionty.base.BFXPipeline method) (bionty.base.BioSample method) (bionty.base.CellLine method) (bionty.base.CellMarker method) (bionty.base.CellType method) (bionty.base.DevelopmentalStage method) (bionty.base.Disease method) (bionty.base.Drug method) (bionty.base.Ethnicity method) (bionty.base.ExperimentalFactor method) (bionty.base.Gene method) (bionty.base.Organism method) (bionty.base.Pathway method) (bionty.base.Phenotype method) (bionty.base.Protein method) (bionty.base.PublicOntology method) (bionty.base.Tissue method) (bionty.CellLine class method) (bionty.CellMarker class method) (bionty.CellType class method) (bionty.core.BioRecord class method) (bionty.core.StaticReference 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) (cellregistry.Cell class method) (clinicore.Biosample class method) (clinicore.ClinicalTrial class method) (clinicore.Medication class method) (clinicore.Patient class method) (clinicore.Treatment class method) (lamindb.core.AnnDataCurator method) (lamindb.core.BaseCurator method) (lamindb.core.CanCurate class method) (lamindb.core.DataFrameCurator method) (lamindb.core.MuDataCurator method) (lamindb.core.QuerySet method) (lamindb.core.SOMACurator method) (lamindb.Curator method) (lamindb.Feature class method) (lamindb.Param class method) (lamindb.ULabel class method) (lamindb.User class method) (ourprojects.Person class method) (ourprojects.Project class method) (ourprojects.Reference class method) (wetlab.Biologic class method) (wetlab.Biosample class method) (wetlab.CombinationPerturbation class method) (wetlab.Compound class method) (wetlab.CompoundPerturbation class method) (wetlab.Donor class method) (wetlab.EnvironmentalPerturbation class method) (wetlab.Experiment class method) (wetlab.GeneticPerturbation class method) (wetlab.PerturbationTarget class method) (wetlab.Techsample class method) (wetlab.Well class method) started_at (lamindb.Run attribute) stat() (lamindb.UPath method) StaticReference (class in bionty.core) status (clinicore.Treatment attribute) STATUS_CHOICES (clinicore.Treatment attribute) stem (lamindb.UPath property) stem_uid (lamindb.Artifact property) (lamindb.Collection property) (lamindb.core.IsVersioned property) (lamindb.core.subsettings.TransformSettings attribute) (lamindb.Transform property) Storage (class in lamindb) storage (lamindb.Artifact attribute) (lamindb.core.Settings property) (lamindb.setup.core.InstanceSettings property) (lamindb.setup.core.SetupSettings property) storage_local (lamindb.core.Settings property) (lamindb.setup.core.InstanceSettings property) storage_options (lamindb.UPath property) StorageSettings (class in lamindb.setup.core) StrField (in module lamindb.core.types) successors (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_all_sources_to_latest() (in module bionty.core) sync_git_repo (lamindb.core.Settings property) synchronize() (lamindb.UPath method) synonym_types() (bionty.base.Ontology 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.Organism attribute) (bionty.Pathway attribute) (bionty.Phenotype attribute) (bionty.Protein attribute) (bionty.Tissue attribute) (clinicore.Medication attribute) (lamindb.Feature attribute) (wetlab.Biologic attribute) (wetlab.Compound attribute) synonyms_mapper (lamindb.core.InspectResult property) system (wetlab.GeneticPerturbation attribute)

T

targets (wetlab.Biologic attribute) (wetlab.CompoundPerturbation attribute) (wetlab.EnvironmentalPerturbation attribute) (wetlab.GeneticPerturbation attribute) Techsample (class in wetlab) terms() (bionty.base.Ontology method) text (ourprojects.Reference attribute) Tissue (class in bionty) (class in bionty.base) tissues (clinicore.Biosample attribute) (wetlab.Biosample attribute) title (clinicore.ClinicalTrial attribute) to_df() (bionty.base.Ontology method) to_dict() (lamindb.core.storage.AnnDataAccessor method) to_memory() (lamindb.core.storage.AnnDataAccessor method) to_pronto() (bionty.base.BFXPipeline method) (bionty.base.BioSample method) (bionty.base.CellLine method) (bionty.base.CellMarker method) (bionty.base.CellType method) (bionty.base.DevelopmentalStage method) (bionty.base.Disease method) (bionty.base.Drug method) (bionty.base.Ethnicity method) (bionty.base.ExperimentalFactor method) (bionty.base.Gene method) (bionty.base.Organism method) (bionty.base.Pathway method) (bionty.base.Phenotype method) (bionty.base.Protein method) (bionty.base.PublicOntology method) (bionty.base.Tissue method) (bionty.core.StaticReference method)

to_url() (lamindb.UPath method) touch() (lamindb.UPath method) track() (in module lamindb) (lamindb.core.Context method) 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.Context property) (lamindb.core.Settings property) (lamindb.Run attribute) transforms (lamindb.ULabel attribute) TransformSettings (class in lamindb.core.subsettings) TransformType (in module lamindb.core.types) Treatment (class in clinicore) type (lamindb.Artifact attribute) (lamindb.setup.core.StorageSettings property) (lamindb.Storage attribute) (lamindb.Transform attribute) (wetlab.Biologic attribute) type_is_cloud (lamindb.setup.core.StorageSettings property)

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.Source attribute) (bionty.Tissue attribute) (cellregistry.Cell attribute) (clinicore.Biosample attribute) (clinicore.ClinicalTrial attribute) (clinicore.Medication attribute) (clinicore.Patient attribute) (clinicore.Treatment attribute) (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.core.Context property) (lamindb.Feature attribute) (lamindb.FeatureSet attribute) (lamindb.Run attribute) (lamindb.setup.core.InstanceSettings property) (lamindb.setup.core.StorageSettings property) (lamindb.setup.core.UserSettings attribute) (lamindb.Storage attribute) (lamindb.Transform attribute) (lamindb.ULabel attribute) (lamindb.User attribute) (ourprojects.Person attribute) (ourprojects.Project attribute) (ourprojects.Reference attribute) (wetlab.Biologic attribute) (wetlab.Biosample attribute) (wetlab.CombinationPerturbation attribute) (wetlab.Compound attribute) (wetlab.CompoundPerturbation attribute) (wetlab.Donor attribute) (wetlab.EnvironmentalPerturbation attribute) (wetlab.Experiment attribute) (wetlab.GeneticPerturbation attribute) (wetlab.PerturbationTarget attribute) (wetlab.Techsample attribute) (wetlab.Well attribute) ULabel (class in lamindb) ulabels (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.Transform attribute) union() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) uniprotkb_id (bionty.CellMarker attribute) (bionty.Protein attribute) unit (lamindb.Feature attribute) (wetlab.EnvironmentalPerturbation attribute) unlink() (lamindb.UPath method) UPath (class in lamindb) UPathStr (in module lamindb.core.types) update() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) update_or_create() (lamindb.core.QueryManager method) (lamindb.core.QuerySet 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) (cellregistry.Cell attribute) (clinicore.Biosample attribute) (clinicore.ClinicalTrial attribute) (clinicore.Medication attribute) (clinicore.Patient attribute) (clinicore.Treatment attribute) (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.Feature attribute) (lamindb.Param attribute) (lamindb.Storage attribute) (lamindb.Transform attribute) (lamindb.ULabel attribute) (lamindb.User attribute) (ourprojects.Person attribute) (ourprojects.Project attribute) (ourprojects.Reference attribute) (wetlab.Biologic attribute) (wetlab.Biosample attribute) (wetlab.CombinationPerturbation attribute) (wetlab.Compound attribute) (wetlab.CompoundPerturbation attribute) (wetlab.Donor attribute) (wetlab.EnvironmentalPerturbation attribute) (wetlab.Experiment attribute) (wetlab.GeneticPerturbation attribute) (wetlab.PerturbationTarget attribute) (wetlab.Techsample attribute) (wetlab.Well attribute)

upload_from() (lamindb.UPath method) url (bionty.Source attribute) (ourprojects.Project attribute) (ourprojects.Reference attribute) use_in_migrations (lamindb.core.QueryManager attribute) User (class in lamindb) user (lamindb.setup.core.SetupSettings property) UserSettings (class in lamindb.setup.core) using() (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.Organism class method) (bionty.Pathway class method) (bionty.Phenotype class method) (bionty.Protein class method) (bionty.Source class method) (bionty.Tissue class method) (cellregistry.Cell class method) (clinicore.Biosample class method) (clinicore.ClinicalTrial class method) (clinicore.Medication class method) (clinicore.Patient class method) (clinicore.Treatment class method) (lamindb.Artifact class method) (lamindb.Collection class method) (lamindb.core.FeatureValue class method) (lamindb.core.ParamValue class method) (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) (lamindb.core.Record class method) (lamindb.core.Registry method) (lamindb.Feature class method) (lamindb.FeatureSet class method) (lamindb.Param class method) (lamindb.Run class method) (lamindb.Storage class method) (lamindb.Transform class method) (lamindb.ULabel class method) (lamindb.User class method) (ourprojects.Person class method) (ourprojects.Project class method) (ourprojects.Reference class method) (wetlab.Biologic class method) (wetlab.Biosample class method) (wetlab.CombinationPerturbation class method) (wetlab.Compound class method) (wetlab.CompoundPerturbation class method) (wetlab.Donor class method) (wetlab.EnvironmentalPerturbation class method) (wetlab.Experiment class method) (wetlab.GeneticPerturbation class method) (wetlab.PerturbationTarget class method) (wetlab.Techsample class method) (wetlab.Well class method)

V

VALID_SUFFIXES (class in lamindb.core.storage) validate() (bionty.base.BFXPipeline method) (bionty.base.BioSample method) (bionty.base.CellLine method) (bionty.base.CellMarker method) (bionty.base.CellType method) (bionty.base.DevelopmentalStage method) (bionty.base.Disease method) (bionty.base.Drug method) (bionty.base.Ethnicity method) (bionty.base.ExperimentalFactor method) (bionty.base.Gene method) (bionty.base.Organism method) (bionty.base.Pathway method) (bionty.base.Phenotype method) (bionty.base.Protein method) (bionty.base.PublicOntology method) (bionty.base.Tissue method) (bionty.CellLine class method) (bionty.CellMarker class method) (bionty.CellType class method) (bionty.core.BioRecord class method) (bionty.core.StaticReference 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) (cellregistry.Cell class method) (clinicore.Biosample class method) (clinicore.ClinicalTrial class method) (clinicore.Medication class method) (clinicore.Patient class method) (clinicore.Treatment class method) (lamindb.core.AnnDataCurator method) (lamindb.core.BaseCurator method) (lamindb.core.CanCurate class method) (lamindb.core.DataFrameCurator method) (lamindb.core.MuDataCurator method) (lamindb.core.QuerySet method) (lamindb.core.SOMACurator method) (lamindb.Curator method) (lamindb.Feature class method) (lamindb.Param class method) (lamindb.ULabel class method) (lamindb.User class method) (ourprojects.Person class method) (ourprojects.Project class method) (ourprojects.Reference class method) (wetlab.Biologic class method) (wetlab.Biosample class method) (wetlab.CombinationPerturbation class method) (wetlab.Compound class method) (wetlab.CompoundPerturbation class method) (wetlab.Donor class method) (wetlab.EnvironmentalPerturbation class method) (wetlab.Experiment class method) (wetlab.GeneticPerturbation class method) (wetlab.PerturbationTarget class method) (wetlab.Techsample class method) (wetlab.Well class method) validated (lamindb.core.InspectResult property) ValidateFields (class in lamindb.core) ValidationError

value (lamindb.core.FeatureValue attribute) (lamindb.core.ParamValue attribute) (wetlab.EnvironmentalPerturbation attribute) values (lamindb.Feature attribute) (lamindb.Param attribute) values() (bionty.base.Ontology method) (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) values_list() (lamindb.core.QueryManager method) (lamindb.core.QuerySet method) var_index (lamindb.core.AnnDataCurator property) (lamindb.core.MuDataCurator property) (lamindb.core.SOMACurator property) var_names (lamindb.core.storage.AnnDataAccessor property) variable verbosity (lamindb.core.Settings property) version (bionty.base.BFXPipeline property) (bionty.base.BioSample property) (bionty.base.CellLine property) (bionty.base.CellMarker property) (bionty.base.CellType property) (bionty.base.DevelopmentalStage property) (bionty.base.Disease property) (bionty.base.Drug property) (bionty.base.Ethnicity property) (bionty.base.ExperimentalFactor property) (bionty.base.Gene property) (bionty.base.Organism property) (bionty.base.Pathway property) (bionty.base.Phenotype property) (bionty.base.Protein property) (bionty.base.PublicOntology property) (bionty.base.Tissue property) (bionty.core.StaticReference property) (bionty.Source attribute) (lamindb.Artifact attribute) (lamindb.Collection attribute) (lamindb.core.Context property) (lamindb.core.subsettings.TransformSettings attribute) (lamindb.Transform attribute) versions (lamindb.Artifact property) (lamindb.Collection property) (lamindb.core.IsVersioned property) (lamindb.Transform property) view() (in module lamindb) view_lineage() (lamindb.Artifact method) (lamindb.Collection method) (lamindb.Transform method) view_parents() (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.Organism method) (bionty.Pathway method) (bionty.Phenotype method) (bionty.Protein method) (bionty.Tissue method) (clinicore.Medication method) (lamindb.core.HasParents method) (lamindb.ULabel method) (wetlab.Compound method) view_tree() (lamindb.UPath method) visibility (lamindb.Artifact attribute) (lamindb.Collection attribute)

W

walk() (lamindb.UPath method) Well (class in wetlab) wetlab module 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)