VisiumIO
This is the released version of VisiumIO; for the devel version, see VisiumIO.
Import Visium data from the 10X Space Ranger pipeline
Bioconductor version: Release (3.23)
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] 
, Estella YiXing Dong [aut, ctb], Dario Righelli [aut, ctb], Helena Crowell [aut, ctb], NCI [fnd] (GrantNo.: U24CA289073)
Maintainer: Marcel Ramos <marcel.ramos at sph.cuny.edu>
citation("VisiumIO")):Marcel Ramos, Estella YiXing Dong, Dario Righelli, Helena Crowell. VisiumIO: Import Visium data from the 10X Space Ranger pipeline. doi:10.18129/B9.bioc.VisiumIO, R package version 1.8.0, https://bioconductor.org/packages/VisiumIO.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text |
Details
| biocViews | DataImport, Infrastructure, SingleCell, Software, Spatial |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.5.0), TENxIO |
| Imports | BiocBaseUtils, BiocGenerics, BiocIO (>= 1.15.1), jsonlite, methods, S4Vectors, sf, SingleCellExperiment, SpatialExperiment, SummarizedExperiment |
| System Requirements | |
| URL | https://github.com/waldronlab/VisiumIO |
| Bug Reports | https://github.com/waldronlab/VisiumIO/issues |
See More
| Suggests | arrow, BiocStyle, data.table, knitr, readr, rmarkdown, tinytest |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | OSTA, XeniumIO |
| Suggests Me | Battlefield, ggspavis, OSTA.data, SpatialExperiment, SpatialFeatureExperiment |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | VisiumIO_1.8.0.tar.gz |
| Windows Binary (x86_64) | VisiumIO_1.8.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | VisiumIO_1.8.0.tgz |
| macOS Binary (sonoma-arm64) | VisiumIO_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/VisiumIO |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/VisiumIO |
| Package Short Url | https://bioconductor.org/packages/VisiumIO/ |
| Package Downloads Report | Download Stats |