# Simple classes and methods for managing Xenium datasets

## Documentation for package ‘xenLite’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

cacheMtif | cache and/or retrieve path to an ome.tif file for demonstration
cacheSfeLungNtx | cache and/or retrieve path to an SFE of V1 lung demo data from 10x
cacheXenLuad | cache and/or retrieve path to Xenium Lung Adenocarcinoma example data, zipped SPEP accompanied by parquet
cacheXenPdmelLite | counts-in-memory version of melanoma 5k dataset
cacheXenProstLite | counts-in-memory version of prostate 5k dataset
clipRect | restrict XenSPEP to cells with centroids in specified rectangle, also restrict boundary and transcript location features
demoapp | simple app to explore an image
e2sym | helper function to map ENS ids to symbols
e79sym | mapping from ENSG to symbols based on EnsDb.Hsapiens.v79
getCellBoundaries | method for cell boundary extraction
getCellBoundaries-method | method for cell boundary extraction
getNucleusBoundaries | method for nucleus boundary extraction
getNucleusBoundaries-method | method for nucleus boundary extraction
getTranscripts | method for transcript extraction
getTranscripts-method | method for transcript extraction
ggprepSeg | prepare a XenSPEP for ggplot2 visualization
ingest_xen | produce a pre-loaded XenSPEP (SpatialExperiment with parquet references)
loadGeometry | read and bind parquet data to XenSPEP
loadGeometry-method | read and bind parquet data to XenSPEP
plotXenGgprep | plot method for ggplot2-prepared XenSPEP
printXenGgprep | print method for ggplot2-prepared XenSPEP
resetParqPaths | utility for dealing with cached Xen_SPEP in temp folder
restoreZipXenSPEP | use unzip, readRDS, and loadGeometry to restore a XenSPEP
show-method | display aspects of XenSPEP
viewSeg | naive polygon viewer
viewSegG2 | naive polygon viewer, will indicate presence of transcripts for two genes in cells
XenSPEP | XenSPEP (SpatialExperiment with parquet references) constructor
XenSPEP-class | manage SpatialExperiment with parquet references
zipXenSPEP | serialize the collection of XenSPEP and parquet with zip
[-method | formal bracket definition, that leaves parquet geometry information alone.