Simple classes and methods for managing Xenium datasets

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Documentation for package ‘xenLite’ version 1.0.0

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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.