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  • Guide
  • API Reference
  • Integrations
  • Changelog

Core

  • CLI
  • Python: lamindb
    • lamindb.track
    • lamindb.finish
    • lamindb.tracked
    • lamindb.Artifact
    • lamindb.Storage
    • lamindb.Transform
    • lamindb.Run
    • lamindb.Feature
    • lamindb.ULabel
    • lamindb.Schema
    • lamindb.Record
    • lamindb.User
    • lamindb.Collection
    • lamindb.Project
    • lamindb.Space
    • lamindb.Branch
    • lamindb.Reference
    • lamindb.Person
    • lamindb.connect
    • lamindb.view
    • lamindb.save
    • lamindb.UPath
    • lamindb.settings
    • lamindb.context
    • lamindb.curators
      • lamindb.curators.DataFrameCurator
      • lamindb.curators.AnnDataCurator
      • lamindb.curators.MuDataCurator
      • lamindb.curators.SpatialDataCurator
      • lamindb.curators.TiledbsomaExperimentCurator
      • lamindb.curators.core
        • lamindb.curators.core.Curator
        • lamindb.curators.core.SlotsCurator
        • lamindb.curators.core.CatVector
        • lamindb.curators.core.CatLookup
        • lamindb.curators.core.DataFrameCatManager
    • lamindb.integrations
      • lamindb.integrations.save_vitessce_config
      • lamindb.integrations.save_tiledbsoma_experiment
    • lamindb.examples
      • lamindb.examples.ingest_mini_immuno_datasets
      • lamindb.examples.schemas
        • lamindb.examples.schemas.valid_features
        • lamindb.examples.schemas.anndata_ensembl_gene_ids_and_valid_features_in_obs
      • lamindb.examples.cellxgene
        • lamindb.examples.cellxgene.save_cxg_defaults
        • lamindb.examples.cellxgene.get_cxg_schema
    • lamindb.errors
      • lamindb.errors.ValidationError
      • lamindb.errors.InvalidArgument
      • lamindb.errors.DoesNotExist
      • lamindb.errors.NotebookNotSaved
      • lamindb.errors.UnknownStorageLocation
      • lamindb.errors.MissingContextUID
      • lamindb.errors.UpdateContext
      • lamindb.errors.IntegrityError
      • lamindb.errors.FieldValidationError
      • lamindb.errors.SQLRecordNameChangeIntegrityError
      • lamindb.errors.NoWriteAccess
    • lamindb.setup
      • lamindb.setup.login
      • lamindb.setup.logout
      • lamindb.setup.init
      • lamindb.setup.disconnect
      • lamindb.setup.delete
      • lamindb.setup.migrate
      • lamindb.setup.settings
      • lamindb.setup.core
        • lamindb.setup.core.SetupSettings
        • lamindb.setup.core.UserSettings
        • lamindb.setup.core.InstanceSettings
        • lamindb.setup.core.StorageSettings
      • lamindb.setup.django
      • lamindb.setup.errors
        • lamindb.setup.errors.InstanceNotSetupError
        • lamindb.setup.errors.ModuleWasntConfigured
        • lamindb.setup.errors.StorageAlreadyManaged
        • lamindb.setup.errors.StorageNotEmpty
        • lamindb.setup.errors.InstanceLockedException
        • lamindb.setup.errors.SettingsEnvFileOutdated
        • lamindb.setup.errors.CannotSwitchDefaultInstance
      • lamindb.setup.types
        • lamindb.setup.types.UPathStr
        • lamindb.setup.types.StorageType
    • lamindb.base
      • lamindb.base.uids
        • lamindb.base.uids.base26
        • lamindb.base.uids.base62
        • lamindb.base.uids.base64
        • lamindb.base.uids.base62_8
        • lamindb.base.uids.base62_12
        • lamindb.base.uids.base62_16
        • lamindb.base.uids.base62_20
      • lamindb.base.types
        • lamindb.base.types.ArtifactKind
        • lamindb.base.types.TransformType
        • lamindb.base.types.Dtype
        • lamindb.base.types.UPathStr
        • lamindb.base.types.StrField
        • lamindb.base.types.ListLike
        • lamindb.base.types.FieldAttr
      • lamindb.base.fields
        • lamindb.base.fields.CharField
        • lamindb.base.fields.TextField
        • lamindb.base.fields.ForeignKey
        • lamindb.base.fields.BooleanField
        • lamindb.base.fields.DateField
        • lamindb.base.fields.DateTimeField
        • lamindb.base.fields.BigIntegerField
        • lamindb.base.fields.IntegerField
        • lamindb.base.fields.OneToOneField
        • lamindb.base.fields.FloatField
        • lamindb.base.fields.DecimalField
        • lamindb.base.fields.BinaryField
        • lamindb.base.fields.JSONField
        • lamindb.base.fields.EmailField
        • lamindb.base.fields.TimeField
        • lamindb.base.fields.SlugField
        • lamindb.base.fields.URLField
        • lamindb.base.fields.UUIDField
        • lamindb.base.fields.PositiveIntegerField
        • lamindb.base.fields.PositiveSmallIntegerField
        • lamindb.base.fields.SmallIntegerField
        • lamindb.base.fields.GenericIPAddressField
        • lamindb.base.fields.DurationField
        • lamindb.base.fields.CharField
        • lamindb.base.fields.TextField
      • lamindb.base.doc_args
      • lamindb.base.deprecated
    • lamindb.core
      • lamindb.core.Settings
      • lamindb.core.subsettings
        • lamindb.core.subsettings.CreationSettings
        • lamindb.core.subsettings.AnnotationSettings
      • lamindb.core.Context
      • lamindb.core.loaders
        • lamindb.core.loaders.SUPPORTED_SUFFIXES
        • lamindb.core.loaders.load_fcs
        • lamindb.core.loaders.load_tsv
        • lamindb.core.loaders.load_h5ad
        • lamindb.core.loaders.load_h5mu
        • lamindb.core.loaders.load_html
        • lamindb.core.loaders.load_json
        • lamindb.core.loaders.load_image
        • lamindb.core.loaders.load_svg
      • lamindb.core.MappedCollection
      • lamindb.core.datasets
        • lamindb.core.datasets.mini_immuno
        • lamindb.core.datasets.anndata_with_obs
        • lamindb.core.datasets.file_fcs
        • lamindb.core.datasets.file_fcs_alpert19
        • lamindb.core.datasets.file_tsv_rnaseq_nfcore_salmon_merged_gene_counts
        • lamindb.core.datasets.file_jpg_paradisi05
        • lamindb.core.datasets.file_tiff_suo22
        • lamindb.core.datasets.file_fastq
        • lamindb.core.datasets.file_bam
        • lamindb.core.datasets.file_mini_csv
        • lamindb.core.datasets.dir_scrnaseq_cellranger
        • lamindb.core.datasets.dir_iris_images
        • lamindb.core.datasets.df_iris
        • lamindb.core.datasets.df_iris_in_meter
        • lamindb.core.datasets.df_iris_in_meter_study1
        • lamindb.core.datasets.df_iris_in_meter_study2
        • lamindb.core.datasets.anndata_mouse_sc_lymph_node
        • lamindb.core.datasets.anndata_human_immune_cells
        • lamindb.core.datasets.anndata_pbmc68k_reduced
        • lamindb.core.datasets.anndata_file_pbmc68k_test
        • lamindb.core.datasets.anndata_pbmc3k_processed
        • lamindb.core.datasets.anndata_with_obs
        • lamindb.core.datasets.anndata_suo22_Visium10X
        • lamindb.core.datasets.mudata_papalexi21_subset
        • lamindb.core.datasets.schmidt22_crispra_gws_IFNG
        • lamindb.core.datasets.schmidt22_perturbseq
        • lamindb.core.datasets.fake_bio_notebook_titles
      • lamindb.core.storage
        • lamindb.core.storage.VALID_SUFFIXES
        • lamindb.core.storage.AnnDataAccessor
        • lamindb.core.storage.BackedAccessor
      • lamindb.core.logger
    • lamindb.models
      • lamindb.models.BaseSQLRecord
      • lamindb.models.SQLRecord
      • lamindb.models.Registry
      • lamindb.models.BasicQuerySet
      • lamindb.models.QuerySet
      • lamindb.models.ArtifactSet
      • lamindb.models.QueryManager
      • lamindb.models.SQLRecordList
      • lamindb.models.FeatureManager
      • lamindb.models.LabelManager
      • lamindb.models.IsVersioned
      • lamindb.models.CanCurate
      • lamindb.models.HasParents
      • lamindb.models.TracksRun
      • lamindb.models.TracksUpdates
      • lamindb.models.FeatureValue
      • lamindb.models.InspectResult
      • lamindb.models.ValidateFields
      • lamindb.models.SchemaOptionals
    • lamindb.Param
    • lamindb.FeatureSet
    • lamindb.Curator
  • R: laminr
    • Setting up LaminR
  • SQL
  • REST

Registry modules

  • bionty
    • bionty.Organism
    • bionty.Gene
    • bionty.Protein
    • bionty.CellMarker
    • bionty.CellType
    • bionty.CellLine
    • bionty.Tissue
    • bionty.Disease
    • bionty.Pathway
    • bionty.Phenotype
    • bionty.ExperimentalFactor
    • bionty.DevelopmentalStage
    • bionty.Ethnicity
    • bionty.settings
    • bionty.Source
    • bionty.core
      • bionty.core.BioRecord
      • bionty.core.StaticReference
      • bionty.core.Settings
      • bionty.core.sync_public_sources
    • bionty.base
      • bionty.base.Organism
      • bionty.base.Gene
      • bionty.base.Protein
      • bionty.base.CellMarker
      • bionty.base.CellType
      • bionty.base.CellLine
      • bionty.base.Tissue
      • bionty.base.Disease
      • bionty.base.Phenotype
      • bionty.base.Pathway
      • bionty.base.ExperimentalFactor
      • bionty.base.DevelopmentalStage
      • bionty.base.Drug
      • bionty.base.Ethnicity
      • bionty.base.BFXPipeline
      • bionty.base.BioSample
      • bionty.base.PublicOntology
      • bionty.base.PublicOntologyField
      • bionty.base.display_sources
      • bionty.base.display_currently_used_sources
      • bionty.base.settings
  • wetlab
    • wetlab.Experiment
    • wetlab.Biosample
    • wetlab.Techsample
    • wetlab.Donor
    • wetlab.GeneticPerturbation
    • wetlab.Biologic
    • wetlab.Compound
    • wetlab.CompoundPerturbation
    • wetlab.EnvironmentalPerturbation
    • wetlab.CombinationPerturbation
    • wetlab.Well
    • wetlab.PerturbationTarget
    • wetlab.GeneticPerturbationSystem
    • wetlab.BiologicType
  • clinicore

lamindb.examples¶

Examples.

ingest_mini_immuno_datasets()

Ingest mini immuno datasets.

schemas

Example schemas.

cellxgene

CELLxGENE utilities.

previous

lamindb.integrations.save_tiledbsoma_experiment

next

lamindb.examples.ingest_mini_immuno_datasets
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