XeniumIO

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

Import and represent Xenium data from the 10X Xenium Analyzer

Platform availability badge Ranking badge Support activity badge Years in BioConductor badge Build results badge Last commit badge Dependency count badge

DOI: 10.18129/B9.bioc.XeniumIO

Bioconductor version: Release (3.22)

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.

Author: Marcel Ramos [aut, cre] ORCID iD ORCID: 0000-0002-3242-0582 , Dario Righelli [ctb], Estella Dong [ctb]

Maintainer: Marcel Ramos <marcel.ramos at sph.cuny.edu>

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

Installation

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


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

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("XeniumIO")

VisiumIO Quick Start Guide HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, Infrastructure, SingleCell, Software, Spatial

Version 1.2.0

In Bioconductor since BioC 3.21 (R-4.5) (0.5 years)

License Artistic-2.0

Depends TENxIO, R (>= 4.5.0)

Imports BiocBaseUtils, BiocGenerics, BiocIO, jsonlite, methods, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, VisiumIO

System Requirements

URL https://github.com/waldronlab/XeniumIO

Bug Reports https://github.com/waldronlab/XeniumIO/issues

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

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 XeniumIO_1.2.0.tar.gz

Windows Binary (x86_64) XeniumIO_1.1.3.zip

macOS Binary (x86_64) XeniumIO_1.2.0.tgz

macOS Binary (arm64) XeniumIO_1.2.0.tgz

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

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

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

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

Package Downloads Report Download Stats