# Lamin Docs

## Guide

  - introduction.md - Introduction
  - tutorial.md - Tutorial
  - setup.md - Install & setup
  - query-search.md - Query, search & stream
    - registries.md - Query & search registries
    - arrays.md - Stream datasets from storage
  - track.md - Manage notebooks, scripts & workflows
  - curate.md - Curate datasets
  - ontologies.md - Access & manage ontologies
    - manage-ontologies.md - Manage biological ontologies
    - public-ontologies.md - Access public ontologies
      - gene.md - Gene
      - protein.md - Protein
      - organism.md - Organism
      - cell_line.md - CellLine
      - cell_type.md - CellType
      - cell_marker.md - CellMarker
      - tissue.md - Tissue
      - disease.md - Disease
      - phenotype.md - Phenotype
      - pathway.md - Pathway
      - experimental_factor.md - ExperimentalFactor
      - developmental_stage.md - DevelopmentalStage
      - ethnicity.md - Ethnicity
  - transfer.md - Transfer data
  - atlases.md - Query & build atlases
    - cellxgene.md - CELLxGENE: scRNA-seq
    - arc-virtual-cell-atlas.md - Arc Virtual Cell Atlas: scRNA-seq
    - hubmap.md - Hubmap
    - rxrx.md - RxRx: cell imaging
  - by-datatype.md - Manage data types
    - scrna.md - scRNA-seq
    - bulkrna.md - Bulk RNA-seq
    - facs.md - Flow cytometry
    - spatial.md - Spatial RNA-seq
    - multimodal.md - Multi-modal
    - ehr.md - EHR
  - by-registry.md - Leverage ontologies
    - celltypist.md - CellTypist
    - enrichr.md - Gene Ontology (GO)
    - analysis-registries.md - Cell type annotation and pathway analysis
    - rdf-sparql.md - RDF export & SPARQL queries
  - trace-data-code.md - Trace data & code
    - schmidt22.md - Re-constructing Schmidt et al. (2022)
  - pipelines.md - Manage computational pipelines
    - nextflow.md - Nextflow
    - redun.md - Redun
    - snakemake.md - Snakemake
  - mlops.md - Manage MLOps
    - wandb.md - Weights & Biases
    - mlflow.md - MLFlow
    - mnist.md - Curate MNIST
    - croissant.md - Croissant
  - visualization.md - Manage visualization dashboards
    - vitessce.md - Vitessce: AnnData
    - vitessce2.md - Vitessce: SpatialData
  - permissions.md - Manage access permissions
  - sheets.md - Work with sheets
  - security.md - Security
  - design.md - Design & architecture
  - faq.md - FAQ
    - faq/pydantic-pandera.md - Pydantic & Pandera vs. LaminDB
    - faq/idempotency.md - Will data get duplicated upon re-running code?
    - faq/acid.md - Will data & metadata stay in sync?
    - faq/track-run-inputs.md - Can I disable tracking run inputs?
    - faq/curate-any.md - How do I validate & annotate arbitrary data structures?
    - faq/import-modules.md - What happens if I import a schema module without lamindb?
    - faq/reference-field.md - Where to store external links and IDs?
    - faq/trash-archive.md - How do I trash or archive objects?
    - faq/keep-artifacts-local.md - Keep artifacts local in a cloud instance
    - faq/validate-fields.md - Django field validation
    - faq/symbol-mapping.md - Why should I not index datasets with gene symbols?
    - faq/search.md - How does search work?
  - influences.md - Influences
  - glossary.md - Glossary

## API Reference

  - cli.md - CLI
  - lamindb.md - Python: "lamindb"
  - laminr.md - R: "laminr"
    - setup-laminr.md - Setting up LaminR
  - sql.md - SQL
  - rest.md - REST
  - bionty.md - bionty
  - pertdb.md - pertdb
  - bionty.cellline.md - bionty.CellLine
  - bionty.cellmarker.md - bionty.CellMarker
  - bionty.models.md - bionty.models
  - bionty.uids.md - bionty.uids
  - lamindb.artifact.md - lamindb.Artifact
  - lamindb.branch.md - lamindb.Branch
  - lamindb.collection.md - lamindb.Collection
  - lamindb.connect.md - lamindb.connect
  - lamindb.context.md - lamindb.context
  - lamindb.curators.md - lamindb.curators
  - lamindb.db.md - lamindb.DB
  - lamindb.examples.md - lamindb.examples
  - lamindb.examples.cellxgene.md - lamindb.examples.cellxgene
  - lamindb.examples.croissant.md - lamindb.examples.croissant
  - lamindb.examples.datasets.md - lamindb.examples.datasets
  - lamindb.examples.datasets.mini_immuno.md - lamindb.examples.datasets.mini_immuno
  - lamindb.examples.mlflow.md - lamindb.examples.mlflow
  - lamindb.examples.schemas.md - lamindb.examples.schemas
  - lamindb.examples.wandb.md - lamindb.examples.wandb
  - lamindb.feature.md - lamindb.Feature
  - lamindb.finish.md - lamindb.finish
  - lamindb.flow.md - lamindb.flow
  - lamindb.integrations.md - lamindb.integrations
  - lamindb.integrations.lightning.md - lamindb.integrations.lightning
  - lamindb.project.md - lamindb.Project
  - lamindb.record.md - lamindb.Record
  - lamindb.reference.md - lamindb.Reference
  - lamindb.run.md - lamindb.Run
  - lamindb.save.md - lamindb.save
  - lamindb.schema.md - lamindb.Schema
  - lamindb.settings.md - lamindb.settings
  - lamindb.space.md - lamindb.Space
  - lamindb.step.md - lamindb.step
  - lamindb.storage.md - lamindb.Storage
  - lamindb.track.md - lamindb.track
  - lamindb.transform.md - lamindb.Transform
  - lamindb.ulabel.md - lamindb.ULabel
  - lamindb.upath.md - lamindb.UPath
  - lamindb.user.md - lamindb.User
  - lamindb.view.md - lamindb.view
  - pertdb.biologic.md - pertdb.Biologic
  - pertdb.biologictype.md - pertdb.BiologicType
  - pertdb.combinationperturbation.md - pertdb.CombinationPerturbation
  - pertdb.compound.md - pertdb.Compound
  - pertdb.compoundperturbation.md - pertdb.CompoundPerturbation
  - pertdb.environmentalperturbation.md - pertdb.EnvironmentalPerturbation
  - pertdb.geneticperturbation.md - pertdb.GeneticPerturbation
  - pertdb.geneticperturbationsystem.md - pertdb.GeneticPerturbationSystem
  - pertdb.perturbationtarget.md - pertdb.PerturbationTarget

## Integrations

- integrations.md - Integrations

## Changelog

- changelog/2022.md - Changelog 2022
- changelog/2023.md - Changelog 2023
- changelog/2024.md - Changelog 2024
- changelog/2025.md - Changelog 2025
- changelog/2026.md - Changelog 2026
- cellxgene-curate.md - Curate "AnnData" based on the CELLxGENE schema
- facs2.md - Append a new dataset
- facs3.md - Query & integrate data
- facs4.md - Analyze the collection and save a result
- nextflow-plugin-reference.md - "nf-lamin" plugin reference
- nextflow-postrun.md - Post-run script
- sc-imaging.md - sc-imaging
- sc-imaging2.md - Generate single-cell images
- sc-imaging3.md - Featurize single-cell images
- sc-imaging4.md - Identify autophagy-positive cells
- scrna-mappedcollection.md - Train a machine learning model on a collection
- scrna-tiledbsoma.md - Concatenate datasets to a single array store
- scrna2.md - Standardize and append a dataset
- scrna3.md - Query artifacts
- scrna4.md - Analyze a collection in memory
- changelog/soon.md - Soon
- spatial2.md - Interactive visualization using Vitessce
- spatial3.md - Curate and ingest spatial data
- spatial4.md - Train a spatial ML model