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This package experimentally explores anS4 class and methods for 10x Xenium demonstration data in Open Storage Network.

BiocManager::install("vjcitn/xenLite")

The package

• defines a classXenSPEP that extends SpatialExperiment, accommodatinggeometry information for cells, nuclei, and transcripts in parquet files thatas of 0.0.17 are ingested byarrow::read_parquet(..., as_data_frame=FALSE).RAM consumption can be significant.

• includes functions to retrieve example data from NSF Open Storage Network buckets

Apkgdown site is available.

A shiny app is available. Some screenshots of earlier versions follow.

The rectangle shows a region of interest, selectable using sliders:

The details can include positions of transcripts for selected genes:

CD4-expressing cells seem spatially complementary to those expressing EPCAM.

An example is available atshinyapps.io.