xenLite

Simple classes and methods for managing Xenium datasets

Bioconductor version: 3.23 · Package version: 1.6.0

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("xenLite")

Details

Maintainer	Vincent Carey <stvjc@channing.harvard.edu>
Author	Vincent Carey [aut, cre] (ORCID: <https://orcid.org/0000-0003-4046-0063>)
License	Artistic-2.0
URL	https://github.com/vjcitn/xenLite
Bug Reports	https://github.com/vjcitn/xenLite/issues
Downloads rank	171
Source branch	RELEASE_3_23
biocViews	Infrastructure, Software

Documentation

xenLite: exploration of a class for Xenium demonstration data

Download

Source package

Dependencies

Depends: R (>= 4.1)

Imports: SpatialExperiment, BiocFileCache, Matrix, S4Vectors, SummarizedExperiment, methods, utils, EBImage, shiny, HDF5Array, arrow, ggplot2, SingleCellExperiment, TENxIO, dplyr, graphics, stats

Suggests: knitr, testthat, BiocStyle, yesno, terra, SpatialFeatureExperiment, SFEData, tiff