XeniumIO

Import and represent Xenium data from the 10X Xenium Analyzer

Bioconductor version: 3.23 · Package version: 1.4.0

The package allows users to readily import spatial data obtained from the 10X Xenium Analyzer pipeline. Supported formats include 'parquet', 'h5', and 'mtx' files. The package mainly represents data as SpatialExperiment objects.

Installation

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

BiocManager::install("XeniumIO")

Details

Maintainer	Marcel Ramos <marcel.ramos@sph.cuny.edu>
Author	Marcel Ramos [aut, cre] (ORCID: <https://orcid.org/0000-0002-3242-0582>), Dario Righelli [ctb], Estella Dong [ctb], NCI [fnd] (GrantNo.: U24CA289073)
License	Artistic-2.0
URL	https://github.com/waldronlab/XeniumIO
Bug Reports	https://github.com/waldronlab/XeniumIO/issues
Downloads rank	270
Source branch	RELEASE_3_23
biocViews	DataImport, Infrastructure, SingleCell, Software, Spatial

Documentation

XeniumIO: Import 10X Genomics Xenium Analyzer Data

Download

Follow the installation instructions to use this package in your R session.

Source package	XeniumIO_1.4.0.tar.gz
Windows binary (x86_64)	XeniumIO_1.4.0.zip
macOS binary (arm64)	XeniumIO_1.4.0.tgz
macOS binary (x86_64)	XeniumIO_1.4.0.tgz

Dependencies

Depends: TENxIO, R (>= 4.5.0)

Imports: BiocBaseUtils, BiocGenerics, BiocIO, jsonlite, methods, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, VisiumIO (>= 1.7.5)

Suggests: arrow, BiocFileCache, BiocStyle, knitr, rmarkdown, tinytest