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  • Guide
  • Reference
  • Changelog

CLI

  • lamin

Core API

  • lamindb
    • lamindb.Artifact
    • lamindb.Collection
    • lamindb.Transform
    • lamindb.Run
    • lamindb.User
    • lamindb.Storage
    • lamindb.ULabel
    • lamindb.Feature
    • lamindb.FeatureSet
    • lamindb.connect
    • lamindb.track
    • lamindb.finish
    • lamindb.Annotate
    • lamindb.view
    • lamindb.save
    • lamindb.integrations
      • lamindb.integrations.save_vitessce_config
    • lamindb.settings
    • lamindb.setup
      • lamindb.setup.login
      • lamindb.setup.logout
      • lamindb.setup.init
      • lamindb.setup.close
      • lamindb.setup.delete
      • lamindb.setup.migrate
      • lamindb.setup.register
      • 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.Registry
      • lamindb.core.QuerySet
      • lamindb.core.QueryManager
      • lamindb.core.RecordsList
      • lamindb.core.HasFeatures
      • lamindb.core.FeatureManager
      • lamindb.core.LabelManager
      • lamindb.core.IsVersioned
      • lamindb.core.CanValidate
      • lamindb.core.HasParents
      • lamindb.core.TracksRun
      • lamindb.core.TracksUpdates
      • lamindb.core.InspectResult
      • lamindb.core.fields
        • lamindb.core.fields.FieldAttr
      • lamindb.core.DataFrameAnnotator
      • lamindb.core.AnnDataAnnotator
      • lamindb.core.MuDataAnnotator
      • lamindb.core.AnnotateLookup
      • lamindb.core.Settings
      • lamindb.core.TransformSettings
      • lamindb.core.MappedCollection
      • lamindb.core.run_context
      • lamindb.core.datasets
        • 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.AnnDataAccessor
        • lamindb.core.storage.BackedAccessor
      • lamindb.core.types
        • lamindb.core.types.UPathStr
        • lamindb.core.types.StrField
        • lamindb.core.types.ListLike
        • lamindb.core.types.TransformType
      • lamindb.core.exceptions
        • lamindb.core.exceptions.ValidationError
        • lamindb.core.exceptions.NotebookNotSavedError
        • lamindb.core.exceptions.NoTitleError
        • lamindb.core.exceptions.MissingTransformSettings
        • lamindb.core.exceptions.UpdateTransformSettings

Plug-ins

  • 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.PublicSource
    • bionty.core
      • bionty.core.BioRegistry
      • bionty.core.PublicOntology
      • bionty.core.Settings
      • bionty.core.sync_all_public_sources_to_latest
      • bionty.core.set_latest_public_sources_as_currently_used
  • wetlab
    • wetlab.Experiment
    • wetlab.ExperimentType
    • wetlab.Biosample
    • wetlab.Techsample
    • wetlab.Treatment
    • wetlab.TreatmentTarget
    • wetlab.Well

Utilities

  • bionty-base
  • readfcs
  • nbproject
  • lamin_utils

lamindb.setup.core.SetupSettings¶

class lamindb.setup.core.SetupSettings¶

Bases: object

Setup settings.

Attributes¶

auto_connect: bool¶

Auto-connect to loaded instance upon lamindb import.

instance: InstanceSettings¶

InstanceSettings.

settings_dir: Path¶
storage: StorageSettings¶

StorageSettings.

user: UserSettings¶

UserSettings.

Methods¶

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lamindb.setup.core

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lamindb.setup.core.UserSettings

  • Attributes
    • auto_connect
    • instance
    • settings_dir
    • storage
    • user
  • Methods
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