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Site Navigation

  • Guide
  • Reference
  • Changelog

Overview

  • Introduction
  • Tutorial: Files & datasets
  • Tutorial: Features & labels

How to

  • Install & setup LaminDB
  • Query & search
    • Query & search registries
    • Query files & datasets
  • Validate data
  • Manage biological registries
  • Manage schemas

Use cases

  • Data flow
    • Project flow
    • Analysis flow
  • Registries
    • CellTypist
    • Gene Ontology (GO)
  • Data types
    • scRNA-seq
      • Integrate scRNA-seq datasets
    • Bulk RNA-seq
    • Flow cytometry
      • Ingest a second file
      • Query & integrate data
      • Analyze a sharded dataset
    • Spatial
    • Multi-modal
  • Pipelines
    • Redun
    • Nextflow
    • Snakemake
  • Atlases
    • cellxgene-census
      • Register cellxgene-census metadata
    • RxRx

Other topics

  • Features
  • FAQ
    • Are LaminDB’s operations idempotent? (What happens if I save the same files & records twice?)
    • Are LaminDB’s operations ACID?
    • Can I disable tracking run inputs?
    • How to track notebooks?
    • What happens when importing lamindb and the instance it not yet setup?
    • What happens if I import a schema module without lamindb?
    • Where to store external links and IDs?
    • Storage FAQ
  • Influences
  • Glossary

Registries#

  • CellTypist
  • Gene Ontology (GO)

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Analysis flow

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CellTypist
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