Query & integrate data¶
import lamindb as ln
import bionty as bt
ln.track("wukchS8V976U0000")
→ connected lamindb: testuser1/test-facs
→ created Transform('wukchS8V976U0000'), started new Run('OOqvMUpF...') at 2025-07-14 06:44:04 UTC
→ notebook imports: bionty==1.6.0 lamindb==1.8.0
Inspect the CellMarker registry
¶
Inspect your aggregated cell marker registry as a DataFrame
:
bt.CellMarker.df().head()
Search for a marker (synonyms aware):
bt.CellMarker.search("PD-1").df().head(2)
Look up markers with auto-complete:
markers = bt.CellMarker.lookup()
markers.cd8
Query artifacts by markers
¶
Query panels and collections based on markers, e.g., which collections have 'CD8'
in the flow panel:
panels_with_cd8 = ln.FeatureSet.filter(cell_markers=markers.cd8).all()
ln.Artifact.filter(feature_sets__in=panels_with_cd8).df()
Access registries:
features = ln.Feature.lookup()
Find shared cell markers between two files:
artifacts = ln.Artifact.filter(feature_sets__in=panels_with_cd8).list()
shared_markers = artifacts[0].features["var"] & artifacts[1].features["var"]
shared_markers.list("name")