XenSCE

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

Installation

BiocManager::install("LTLA/ParquetDataFrame") # DelayedArray approach
BiocManager::install("vjcitn/XenSCE")

Basics

The package

• defines a class XenSCE that extends SingleCellExperiment, accommodating geometry information for cells, nuclei, and transcripts in ParquetDataFrame or DataFrame instances

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

• includes a small example panc_sub derived from SFEData XeniumOutput

A view of the panc_sub XenSCE:

Compare to the morphology_focus_0001.ome.tif found in the morphology_focus component of SFEData XeniumOutput

A pkgdown site is available.

Interaction

A shiny app is available in inst/app3 of the sources.

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

The details can include positions of transcripts for selected genes:

CD4-expressing cells seem complementary to those expressing EPCAM.

An example is available at shinyapps.io.

Another example with a 5K panel is available at shinyapps.io.