Package: xenLite 1.1.0

Vincent Carey

xenLite: Simple classes and methods for managing Xenium datasets

Define a relatively light class for managing Xenium data using Bioconductor. Address use of parquet for coordinates, SpatialExperiment for assay and sample data. Address serialization and use of cloud storage.

Authors:Vincent Carey [aut, cre]

xenLite_1.1.0.tar.gz
xenLite_1.1.0.zip(r-4.5)xenLite_1.1.0.zip(r-4.4)xenLite_1.1.0.zip(r-4.3)
xenLite_1.1.0.tgz(r-4.4-any)xenLite_1.1.0.tgz(r-4.3-any)
xenLite_1.1.0.tar.gz(r-4.5-noble)xenLite_1.1.0.tar.gz(r-4.4-noble)
xenLite_1.1.0.tgz(r-4.4-emscripten)xenLite_1.1.0.tgz(r-4.3-emscripten)
xenLite.pdf |xenLite.html✨
xenLite/json (API)

# Install 'xenLite' in R:
install.packages('xenLite', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/vjcitn/xenlite/issues

Datasets:
  • e79sym - Mapping from ENSG to symbols based on EnsDb.Hsapiens.v79

On BioConductor:xenLite-1.1.0(bioc 3.21)xenLite-1.0.0(bioc 3.20)

infrastructure

4.48 score 1 stars 4 scripts 21 exports 129 dependencies

Last updated 2 months agofrom:921c0573b7. Checks:OK: 1 NOTE: 4 ERROR: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 30 2024
R-4.5-winNOTENov 30 2024
R-4.5-linuxNOTENov 30 2024
R-4.4-winNOTENov 30 2024
R-4.4-macNOTENov 30 2024
R-4.3-winERRORNov 30 2024
R-4.3-macERRORNov 30 2024

Exports:cacheMtifcacheXenLuadcacheXenPdmelLitecacheXenProstLiteclipRectdemoappe2symgetCellBoundariesgetNucleusBoundariesgetTranscriptsggprepSegingest_xenloadGeometryplotXenGgprepresetParqPathsrestoreZipXenSPEPshowviewSegviewSegG2XenSPEPzipXenSPEP

Dependencies:abindarrowaskpassassertthatbase64encBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObitbit64bitopsblobbslibcachemclicliprcolorspacecommonmarkcpp11crayoncurlDBIdbplyrDelayedArraydigestdplyrEBImageevaluatefansifarverfastmapfftwtoolsfilelockfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtableHDF5ArrayhighrhmshtmltoolshtmlwidgetshttpuvhttrIRangesisobandjpegjquerylibjsonliteknitrlabelinglaterlatticelifecyclelocfitmagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngprettyunitsprogresspromisespurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrrhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownRSQLiteS4ArraysS4VectorssassscalesshinySingleCellExperimentsourcetoolsSparseArraySpatialExperimentstringistringrSummarizedExperimentsysTENxIOtibbletidyrtidyselecttifftinytextzdbUCSC.utilsutf8vctrsviridisLitevroomwithrxfunxtableXVectoryamlzlibbioc

xenLite: exploration of a class for Xenium demonstration data

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered fromxenLite.Rmdusingknitr::rmarkdownon Nov 30 2024.

Last update: 2024-09-29
Started: 2024-09-07

Readme and manuals

Help Manual

Help pageTopics
formal bracket definition, that leaves parquet geometry information alone.[,XenSPEP,ANY,ANY,ANY-method
cache and/or retrieve path to an ome.tif file for demonstrationcacheMtif
cache and/or retrieve path to an SFE of V1 lung demo data from 10xcacheSfeLungNtx
cache and/or retrieve path to Xenium Lung Adenocarcinoma example data, zipped SPEP accompanied by parquetcacheXenLuad
counts-in-memory version of melanoma 5k datasetcacheXenPdmelLite
counts-in-memory version of prostate 5k datasetcacheXenProstLite
restrict XenSPEP to cells with centroids in specified rectangle, also restrict boundary and transcript location featuresclipRect
simple app to explore an imagedemoapp
helper function to map ENS ids to symbolse2sym
mapping from ENSG to symbols based on EnsDb.Hsapiens.v79e79sym
method for cell boundary extractiongetCellBoundaries
method for cell boundary extractiongetCellBoundaries,XenSPEP-method
method for nucleus boundary extractiongetNucleusBoundaries
method for nucleus boundary extractiongetNucleusBoundaries,XenSPEP-method
method for transcript extractiongetTranscripts
method for transcript extractiongetTranscripts,XenSPEP-method
prepare a XenSPEP for ggplot2 visualizationggprepSeg
produce a pre-loaded XenSPEP (SpatialExperiment with parquet references)ingest_xen
read and bind parquet data to XenSPEPloadGeometry
read and bind parquet data to XenSPEPloadGeometry,XenSPEP-method
plot method for ggplot2-prepared XenSPEPplotXenGgprep
print method for ggplot2-prepared XenSPEPprintXenGgprep
utility for dealing with cached Xen_SPEP in temp folderresetParqPaths
use unzip, readRDS, and loadGeometry to restore a XenSPEPrestoreZipXenSPEP
display aspects of XenSPEPshow,XenSPEP-method
naive polygon viewerviewSeg
naive polygon viewer, will indicate presence of transcripts for two genes in cellsviewSegG2
XenSPEP (SpatialExperiment with parquet references) constructorXenSPEP
manage SpatialExperiment with parquet referencesXenSPEP-class
serialize the collection of XenSPEP and parquet with zipzipXenSPEP