Simple classes and methods for managing Xenium datasets • xenLite

This package experimentally explores an S4 class and methods for 10x Xenium demonstration data in Open Storage Network.

Installation

BiocManager::install("vjcitn/xenLite")

The package

defines a class XenSPEP that extends SpatialExperiment, accommodating geometry information for cells, nuclei, and transcripts in parquet files that as of 0.0.17 are ingested by arrow::read_parquet(..., as_data_frame=FALSE). RAM consumption can be significant.
includes functions to retrieve example data from NSF Open Storage Network buckets

A pkgdown 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 at shinyapps.io.