xenLite

This is the released version of xenLite; for the devel version, see xenLite.

Simple classes and methods for managing Xenium datasets

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DOI: 10.18129/B9.bioc.xenLite

Bioconductor version: Release (3.22)

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.

Author: Vincent Carey [aut, cre] ORCID iD ORCID: 0000-0003-4046-0063

Maintainer: Vincent Carey <stvjc at channing.harvard.edu>

Citation (from within R, enter citation("xenLite")):

Installation

To install this package, start R (version "4.5") and enter:


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

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("xenLite")

xenLite: exploration of a class for Xenium demonstration data HTML R Script

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Infrastructure, Software

Version 1.4.0

In Bioconductor since BioC 3.20 (R-4.4) (1 year)

License Artistic-2.0

Depends R (>= 4.1)

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

System Requirements

URL https://github.com/vjcitn/xenLite

Bug Reports https://github.com/vjcitn/xenLite/issues

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

Linking To

Enhances

Depends On Me

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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package xenLite_1.4.0.tar.gz

Windows Binary (x86_64) xenLite_1.3.0.zip

macOS Binary (x86_64) xenLite_1.4.0.tgz

macOS Binary (arm64) xenLite_1.4.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/xenLite

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/xenLite

Bioc Package Browser https://code.bioconductor.org/browse/xenLite/

Package Short Url https://bioconductor.org/packages/xenLite/

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