# Lamin Docs ## Guide ### Overview - [Introduction](introduction.md) - [Tutorial](tutorial.md) ### How to - [Install & setup](setup.md) - [Query & search](query-search.md) - [Query tables in storage](tables.md) - [Query arrays in storage](arrays.md) - [Track notebooks, scripts & workflows](track.md) - [Organize datasets](organize.md) - [Curate datasets](curate.md) - [Manage changes](manage-changes.md) - [Manage records & ontologies](manage-records.md) - [Manage biological ontologies](manage-ontologies.md) - [Public biological ontologies](public-ontologies.md) - [Gene](gene.md) - [Protein](protein.md) - [Organism](organism.md) - [CellLine](cell_line.md) - [CellType](cell_type.md) - [CellMarker](cell_marker.md) - [Tissue](tissue.md) - [Disease](disease.md) - [Phenotype](phenotype.md) - [Pathway](pathway.md) - [ExperimentalFactor](experimental_factor.md) - [DevelopmentalStage](developmental_stage.md) - [Ethnicity](ethnicity.md) - [Transfer & sync across databases](transfer.md) ### Use cases - [Agentic analyses](analyses.md) - [Target prioritization](target-prioritization.md) - [Copy-number variation](copy-number-variation.md) - [Perturbation modeling](perturbation-modeling.md) - [Scanpy analysis](scanpy-analysis.md) - [Query & build atlases](atlases.md) - [1000 Genomes](1000genomes.md) - [Arc Virtual Cell Atlas](arc-virtual-cell-atlas.md) - [CELLxGENE](cellxgene.md) - [Curate "AnnData" based on the CELLxGENE schema](cellxgene-curate.md) - [EWAS Data Hub](ewas-datahub.md) - [Hubmap](hubmap.md) - [RxRx](rxrx.md) - [Manage data types](by-datatype.md) - [scRNA-seq](scrna.md) - [Standardize and append a dataset](scrna2.md) - [Query artifacts](scrna3.md) - [Analyze a collection in memory](scrna4.md) - [Use machine learning data loaders](scrna-dataloading.md) - [Concatenate datasets to a single array store](scrna-tiledbsoma.md) - [Preprocessing and clustering 3k PBMCs](pbmc3k.md) - [Bulk RNA-seq](bulkrna.md) - [Methylation](dna-methylation.md) - [Genomic variants](genomic-variants.md) - [Flow cytometry](facs.md) - [Append a new dataset](facs2.md) - [Query & integrate data](facs3.md) - [Analyze the collection and save a result](facs4.md) - [Spatial RNA-seq](spatial.md) - [Interactive visualization using Vitessce](spatial2.md) - [Curate and ingest spatial data](spatial3.md) - [Train a spatial ML model](spatial4.md) - [Single-cell imaging](sc-imaging.md) - [Generate single-cell images](sc-imaging2.md) - [Featurize single-cell images](sc-imaging3.md) - [Identify autophagy-positive cells](sc-imaging4.md) - [Multi-modal](multimodal.md) - [EHR](ehr.md) - [Leverage ontologies](by-registry.md) - [CellTypist](celltypist.md) - [Gene Ontology (GO)](enrichr.md) - [Cell type annotation and pathway analysis](analysis-registries.md) - [RDF export & SPARQL queries](rdf-sparql.md) - [Manage computational pipelines](pipelines.md) - [Nextflow](nextflow.md) - [Redun](redun.md) - [Snakemake](snakemake.md) - [Manage MLOps](mlops.md) - [Lightning](lightning.md) - [Curate MNIST](mnist.md) - [Weights & Biases](wandb.md) - [MLFlow](mlflow.md) - [ClearML](clearml.md) - [Croissant](croissant.md) - [Manage visualization dashboards](visualization.md) - [Vitessce: AnnData](vitessce.md) - [Vitessce: SpatialData](vitessce2.md) ### The Hub - [Launch functions & pipelines](launch.md) - [Access permissions](permissions.md) - [Audit log](audit-log.md) - [Security](security.md) ### Other topics - [Architecture](architecture.md) - [Will data & metadata stay in sync?](acid.md) - [Will data get duplicated upon re-running code?](idempotency.md) - [FAQ](faq.md) - [Pydantic, Pandera, and LaminDB](faq/pydantic-pandera.md) - [Can I disable tracking run inputs?](faq/track-run-inputs.md) - [How do I validate & annotate arbitrary data structures?](faq/curate-any.md) - [Keep artifacts local in a cloud instance](faq/keep-artifacts-local.md) - [Why should I not index datasets with gene symbols?](faq/symbol-mapping.md) - [How does search work?](faq/search.md) - [Influences](influences.md) - [Glossary](glossary.md) ## API Reference - [CLI](cli.md) - [Python: "lamindb"](lamindb.md) - [lamindb.Artifact](lamindb.artifact.md) - [lamindb.Branch](lamindb.branch.md) - [lamindb.Collection](lamindb.collection.md) - [lamindb.connect](lamindb.connect.md) - [lamindb.context](lamindb.context.md) - [lamindb.curators](lamindb.curators.md) - [lamindb.DB](lamindb.db.md) - [lamindb.examples](lamindb.examples.md) - [lamindb.examples.cellxgene](lamindb.examples.cellxgene.md) - [lamindb.examples.croissant](lamindb.examples.croissant.md) - [lamindb.examples.datasets](lamindb.examples.datasets.md) - [lamindb.examples.datasets.mini_immuno](lamindb.examples.datasets.mini_immuno.md) - [lamindb.examples.mlflow](lamindb.examples.mlflow.md) - [lamindb.examples.schemas](lamindb.examples.schemas.md) - [lamindb.examples.wandb](lamindb.examples.wandb.md) - [lamindb.Feature](lamindb.feature.md) - [lamindb.finish](lamindb.finish.md) - [lamindb.flow](lamindb.flow.md) - [lamindb.integrations](lamindb.integrations.md) - [lamindb.integrations.lightning](lamindb.integrations.lightning.md) - [lamindb.integrations.notion](lamindb.integrations.notion.md) - [lamindb.Project](lamindb.project.md) - [lamindb.Record](lamindb.record.md) - [lamindb.Reference](lamindb.reference.md) - [lamindb.Run](lamindb.run.md) - [lamindb.save](lamindb.save.md) - [lamindb.Schema](lamindb.schema.md) - [lamindb.settings](lamindb.settings.md) - [lamindb.Space](lamindb.space.md) - [lamindb.step](lamindb.step.md) - [lamindb.Storage](lamindb.storage.md) - [lamindb.track](lamindb.track.md) - [lamindb.Transform](lamindb.transform.md) - [lamindb.ULabel](lamindb.ulabel.md) - [lamindb.UPath](lamindb.upath.md) - [lamindb.User](lamindb.user.md) - [lamindb.view](lamindb.view.md) - [R: "laminr"](laminr.md) - [Setting up LaminR](setup-laminr.md) - [Nextflow: "nf-lamin"](nf-lamin.md) - [Nextflow config](nf-lamin/config.md) - [Functions](nf-lamin/functions.md) - [Lamin URIs](nf-lamin/lamin-uri.md) - [Examples](nf-lamin/examples.md) - [SQL](sql.md) - [REST](rest.md) - [Authentication](hub/authentication.md) - [Service endpoints and IP whitelisting](hub/service-endpoints.md) - [MCP](mcp.md) - [bionty](bionty.md) - [bionty.CellLine](bionty.cellline.md) - [bionty.CellMarker](bionty.cellmarker.md) - [bionty.models](bionty.models.md) - [bionty.uids](bionty.uids.md) - [pertdb](pertdb.md) - [pertdb.Biologic](pertdb.biologic.md) - [pertdb.BiologicType](pertdb.biologictype.md) - [pertdb.CombinationPerturbation](pertdb.combinationperturbation.md) - [pertdb.Compound](pertdb.compound.md) - [pertdb.CompoundPerturbation](pertdb.compoundperturbation.md) - [pertdb.EnvironmentalPerturbation](pertdb.environmentalperturbation.md) - [pertdb.GeneticPerturbation](pertdb.geneticperturbation.md) - [pertdb.GeneticPerturbationSystem](pertdb.geneticperturbationsystem.md) - [pertdb.PerturbationTarget](pertdb.perturbationtarget.md) ## Integrations - [Integrations](integrations.md) ## Changelog - [Changelog 2022](changelog/2022.md) - [Changelog 2023](changelog/2023.md) - [Changelog 2024](changelog/2024.md) - [Changelog 2025](changelog/2025.md) - [Changelog 2026](changelog/2026.md) - [Soon](changelog/soon.md)