VisiumIO

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see VisiumIO.

Import Visium data from the 10X Space Ranger pipeline

Bioconductor version: 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")
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

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, Infrastructure, SingleCell, Software, Spatial

Version 1.0.0

In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)

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

Suggests BiocStyle, knitr, rmarkdown, tinytest

Linking To

Enhances

Depends On Me

Imports Me

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Links To Me

Build Report Build Report

Package Archives

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

Source Package VisiumIO_1.0.0.tar.gz

Windows Binary (x86_64) VisiumIO_1.0.0.zip (64-bit only)

macOS Binary (x86_64) VisiumIO_1.0.0.tgz

macOS Binary (arm64) VisiumIO_1.0.0.tgz

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/

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