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  • Guide
  • API
  • Integrations
  • Changelog

CLI & lamindb

  • lamin
  • lamindb
    • lamindb.Artifact
    • lamindb.Collection
    • lamindb.Transform
    • lamindb.Run
    • lamindb.User
    • lamindb.Storage
    • lamindb.ULabel
    • lamindb.Feature
    • lamindb.FeatureSet
    • lamindb.Param
    • lamindb.track
    • lamindb.finish
    • lamindb.connect
    • lamindb.Curator
    • lamindb.view
    • lamindb.save
    • lamindb.integrations
      • lamindb.integrations.save_vitessce_config
      • lamindb.integrations.save_tiledbsoma_experiment
    • lamindb.context
    • lamindb.settings
    • lamindb.setup
      • lamindb.setup.login
      • lamindb.setup.logout
      • lamindb.setup.init
      • lamindb.setup.close
      • 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.UPath
    • lamindb.core
      • lamindb.core.Record
      • lamindb.core.Registry
      • lamindb.core.QuerySet
      • lamindb.core.QueryManager
      • lamindb.core.RecordList
      • lamindb.core.FeatureManager
      • lamindb.core.ParamManager
      • lamindb.core.LabelManager
      • lamindb.core.IsVersioned
      • lamindb.core.CanCurate
      • lamindb.core.HasParents
      • lamindb.core.TracksRun
      • lamindb.core.TracksUpdates
      • lamindb.core.ParamValue
      • lamindb.core.FeatureValue
      • lamindb.core.InspectResult
      • lamindb.core.ValidateFields
      • lamindb.core.fields
        • lamindb.core.fields.FieldAttr
      • lamindb.core.BaseCurator
      • lamindb.core.DataFrameCurator
      • lamindb.core.AnnDataCurator
      • lamindb.core.MuDataCurator
      • lamindb.core.SOMACurator
      • lamindb.core.CurateLookup
      • lamindb.core.Settings
      • lamindb.core.Context
      • lamindb.core.MappedCollection
      • 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.datasets
        • lamindb.core.datasets.small_dataset1
        • lamindb.core.datasets.small_dataset2
        • 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.types
        • lamindb.core.types.ArtifactType
        • lamindb.core.types.TransformType
        • lamindb.core.types.FeatureDtype
        • lamindb.core.types.UPathStr
        • lamindb.core.types.StrField
        • lamindb.core.types.ListLike
      • lamindb.core.exceptions
        • lamindb.core.exceptions.InvalidArgument
        • lamindb.core.exceptions.DoesNotExist
        • lamindb.core.exceptions.ValidationError
        • lamindb.core.exceptions.NotebookNotSaved
        • lamindb.core.exceptions.NoTitleError
        • lamindb.core.exceptions.MissingContextUID
        • lamindb.core.exceptions.UpdateContext
        • lamindb.core.exceptions.IntegrityError
        • lamindb.core.exceptions.RecordNameChangeIntegrityError
      • lamindb.core.subsettings
        • lamindb.core.subsettings.TransformSettings
        • lamindb.core.subsettings.CreationSettings
      • lamindb.core.logger

R & REST

  • laminr
  • REST

Schema 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_all_sources_to_latest
      • bionty.core.set_latest_sources_as_currently_used
    • 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_available_sources
      • bionty.base.display_currently_used_sources
      • bionty.base.reset_sources
      • bionty.base.settings
      • bionty.base.Ontology
  • ourprojects
    • ourprojects.Person
    • ourprojects.Project
    • ourprojects.Reference
  • 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
    • clinicore.Biosample
    • clinicore.ClinicalTrial
    • clinicore.Medication
    • clinicore.Patient
    • clinicore.Treatment
  • cellregistry
    • cellregistry.Cell
  • omop

lamindb.integrations¶

Integrations.

save_vitessce_config(vitessce_config[, ...])

Validates and saves a VitessceConfig object.

save_tiledbsoma_experiment(adatas[, key, ...])

Write AnnData to tiledbsoma.Experiment.

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lamindb.save

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lamindb.integrations.save_vitessce_config
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