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VisiumIO

This is the development version of VisiumIO; to use it, please install the devel version of Bioconductor.

Import Visium data from the 10X Space Ranger pipeline


Bioconductor version: Development (3.19)

The package allows users to readily import spatial data obtained from either the 10X website or from the Space Ranger pipeline. Supported formats include tar.gz, h5, and mtx files. Multiple files can be imported at once with *List type of functions. The package represents data mainly as SpatialExperiment objects.

Author: Marcel Ramos [aut, cre]

Maintainer: Marcel Ramos <marcel.ramos at roswellpark.org>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("VisiumIO")

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("VisiumIO")
VisiumIO Quick Start Guide HTML R Script
Reference Manual PDF

Details

biocViews DataImport, Infrastructure, SingleCell, Software, Spatial
Version 0.99.3
In Bioconductor since BioC 3.19 (R-4.4)
License Artistic-2.0
Depends R (>= 4.4.0), TENxIO
Imports BiocBaseUtils, BiocGenerics, BiocIO, jsonlite, methods, S4Vectors, SpatialExperiment, SummarizedExperiment
System Requirements
URL https://github.com/waldronlab/VisiumIO
Bug Reports https://github.com/waldronlab/VisiumIO/issues
See More
Suggests BiocStyle, knitr, rmarkdown, tinytest
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Build Report Build Report

Package Archives

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

Source Package VisiumIO_0.99.3.tar.gz
Windows Binary VisiumIO_0.99.3.zip
macOS Binary (x86_64) VisiumIO_0.99.3.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/VisiumIO
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/VisiumIO
Bioc Package Browser https://code.bioconductor.org/browse/VisiumIO/
Package Short Url https://bioconductor.org/packages/VisiumIO/
Package Downloads Report Download Stats