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Site Navigation

  • Guide
  • API
  • Integrations
  • Changelog

Overview

  • Introduction
  • Tutorial: Artifacts
  • Tutorial: Features & labels

How to

  • Install & setup
  • Query & search
    • Query & search registries
    • Query arrays
  • Track notebooks & scripts
  • Curate datasets
    • Curate DataFrames and AnnDatas
    • Curate datasets of any format
    • Enforce pre-defined validation constraints
  • Access public ontologies
    • Gene
    • Protein
    • Organism
    • CellLine
    • CellType
    • CellMarker
    • Tissue
    • Disease
    • Phenotype
    • Pathway
    • ExperimentalFactor
    • DevelopmentalStage
    • Ethnicity
  • Manage biological registries
  • Manage schema modules
  • Transfer data

Use cases

  • Atlases
    • CELLxGENE: scRNA-seq
      • Curate AnnData based on the CELLxGENE schema
    • RxRx: cell imaging
  • Data types
    • scRNA-seq
      • Standardize and append a dataset
      • Query artifacts
      • Analyze a collection in memory
      • Train a machine learning model on a collection
      • Concatenate datasets to a single array store
    • Bulk RNA-seq
    • Flow cytometry
      • Append a new dataset
      • Query & integrate data
      • Analyze the collection and save a result
    • Spatial
    • Multi-modal
    • Perturbation
  • Registries
    • Gene Ontology (GO)
    • CellTypist
    • Standardize metadata on-the-fly
    • RDF export & SPARQL queries
  • Data lineage
    • Project flow
      • GWS CRIPSRa analysis
      • Perform single cell analysis, integrate with CRISPRa screen
    • Analysis flow
  • Pipelines – workflow managers
    • Redun
    • Nextflow
    • Snakemake
  • MLOps
    • Weights & Biases
    • Curate MNIST
  • Visualization
    • Vitessce

Key topics

  • Access management
  • Security
  • FAQ
    • What happens if I save the same artifacts & records twice?
    • Will data & metadata stay in sync?
    • Can I disable tracking run inputs?
    • What happens when importing lamindb and the instance is not yet setup?
    • What happens if I import a schema module without lamindb?
    • Where to store external links and IDs?
    • What does the key parameter do under the hood?
    • When do visibility of artifacts and collections change?
    • How to delete records?
    • Keep artifacts local in a cloud instance
    • Django field validation
    • Why should I validate against gene symbols?
    • How does search work?
    • Storage FAQ
  • Influences
  • Glossary

Visualization¶

  • Vitessce

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Curate MNIST

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Vitessce
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