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Guide
Reference
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Site Navigation
Guide
Reference
Changelog
GitHub
Overview
Introduction
Tutorial: Artifacts
Tutorial: Features & labels
How to
Install & setup
Query & search
Query & search registries
Query arrays
Track notebooks & scripts
Validate, standardize & annotate
Validate & standardize for developers
Annotate data for developers
Access public biological ontologies
Gene
Protein
Organism
CellLine
CellType
Cell marker
Tissue
Disease
Phenotype
Pathway
ExperimentalFactor
DevelopmentalStage
Ethnicity
Manage biological registries
Manage schemas
Transfer data
Use cases
Atlases
CELLxGENE: scRNA-seq
Query cellxgene-census using TileDB-SOMA
Annotate an h5ad file based on CELLxGENE schema
RxRx: cell imaging
Data types
scRNA-seq
Standardize and append a batch of data
Query artifacts
Analyze a collection in memory
Train a machine learning model on a collection
Transform a number of array shards 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
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
Redun
Nextflow
Snakemake
Integrations
Vitessce
Key topics
Features
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
Storage FAQ
Influences
Glossary
Guide
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