xenLite
This is the development version of xenLite; for the stable release version, see xenLite.
Simple classes and methods for managing Xenium datasets
Bioconductor version: Development (3.21)
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:
Maintainer: Vincent Carey <stvjc at channing.harvard.edu>
citation("xenLite")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 |
Details
| biocViews | Infrastructure, Software |
| Version | 1.1.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (< 6 months) |
| 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 |
See More
| Suggests | knitr, testthat, BiocStyle, yesno, terra, SpatialFeatureExperiment, SFEData, tiff |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | xenLite_1.1.0.tar.gz |
| Windows Binary (x86_64) | xenLite_1.1.0.zip |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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/ |
| Package Downloads Report | Download Stats |