Package: xenLite 0.99.5

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_0.99.5.tar.gz
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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'))

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

Datasets:

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

On BioConductor:xenLite-0.99.4(bioc 3.20)

infrastructure

4.40 score 1 stars 4 scripts 21 exports 129 dependencies

Last updated 7 days agofrom:497a063215. Checks:OK: 1 NOTE: 4 ERROR: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 17 2024
R-4.5-win	NOTE	Oct 17 2024
R-4.5-linux	NOTE	Oct 17 2024
R-4.4-win	NOTE	Oct 17 2024
R-4.4-mac	NOTE	Oct 17 2024
R-4.3-win	ERROR	Oct 17 2024
R-4.3-mac	ERROR	Oct 17 2024

Exports:cacheMtif cacheXenLuad cacheXenPdmelLite cacheXenProstLite clipRect demoapp e2sym getCellBoundaries getNucleusBoundaries getTranscripts ggprepSeg ingest_xen loadGeometry plotXenGgprep resetParqPaths restoreZipXenSPEP show viewSeg viewSegG2 XenSPEP zipXenSPEP

Dependencies:abind arrow askpass assertthat base64enc Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO bit bit64 bitops blob bslib cachem cli clipr colorspace commonmark cpp11 crayon curl DBI dbplyr DelayedArray digest dplyr EBImage evaluate fansi farver fastmap fftwtools filelock fontawesome fs generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable HDF5Array highr hms htmltools htmlwidgets httpuv httr IRanges isoband jpeg jquerylib jsonlite knitr labeling later lattice lifecycle locfit magick magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr png prettyunits progress promises purrr R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RCurl readr rhdf5 rhdf5filters Rhdf5lib rjson rlang rmarkdown RSQLite S4Arrays S4Vectors sass scales shiny SingleCellExperiment sourcetools SparseArray SpatialExperiment stringi stringr SummarizedExperiment sys TENxIO tibble tidyr tidyselect tiff tinytex tzdb UCSC.utils utf8 vctrs viridisLite vroom withr xfun xtable XVector yaml zlibbioc

xenLite: exploration of a class for Xenium demonstration data

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

Rendered fromxenLite.Rmdusingknitr::rmarkdownon Oct 17 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

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