| 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. |