https://github.com/vjcitn/xenlite

Lightweight approach to managing Xenium experiments
https://github.com/vjcitn/xenlite

u24ca289073

Last synced: about 2 months ago
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Lightweight approach to managing Xenium experiments

• Host: GitHub
• URL: https://github.com/vjcitn/xenlite
• Owner: vjcitn
• Created: 2024-09-07T19:45:15.000Z (9 months ago)
• Default Branch: main
• Last Pushed: 2024-11-27T11:41:03.000Z (7 months ago)
• Last Synced: 2025-04-11T13:16:24.457Z (2 months ago)
• Topics: u24ca289073
• Language: R
• Homepage: https://vjcitn.github.io/xenLite/
• Size: 15.8 MB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md

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README

        
# xenLite

This package experimentally explores an

S4 class and methods for 10x Xenium demonstration data in Open Storage Network.

## Installation

```

BiocManager::install("vjcitn/xenLite")

```

## Basics

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](https://vjcitn.github.io/xenLite) is available.

## Interaction

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

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

![](man/figures/nappma2.png)

The details can include positions of transcripts for selected genes:

![](man/figures/napp2.png)

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

![](man/figures/nappcd.png)

An example is available at [shinyapps.io](https://vjcitn.shinyapps.io/XenLUAD).