SpatialExperimentIO
This is the development version of SpatialExperimentIO; to use it, please install the devel version of Bioconductor.
Read in Xenium, CosMx, MERSCOPE or STARmapPLUS data as SpatialExperiment object
Bioconductor version: Development (3.21)
Read in imaging-based spatial transcriptomics technology data. Current available modules are for Xenium by 10X Genomics, CosMx by Nanostring, MERSCOPE by Vizgen, or STARmapPLUS from Broad Institute. You can choose to read the data in as a SpatialExperiment or a SingleCellExperiment object.
Author: Yixing E. Dong [aut, cre] (ORCID:
Maintainer: Yixing E. Dong <estelladong729 at gmail.com>
citation("SpatialExperimentIO")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("SpatialExperimentIO")
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("SpatialExperimentIO")| SpatialExperimentIO Reader Package Overview | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, DataRepresentation, GeneExpression, Infrastructure, SingleCell, Software, Spatial, Transcriptomics |
| Version | 0.99.7 |
| In Bioconductor since | BioC 3.21 (R-4.5) |
| License | Artistic-2.0 |
| Depends | |
| Imports | DropletUtils, SpatialExperiment, SingleCellExperiment, methods, data.table, arrow, purrr, S4Vectors |
| System Requirements | |
| URL | https://github.com/estellad/SpatialExperimentIO |
| Bug Reports | https://github.com/estellad/SpatialExperimentIO/issues |
See More
| Suggests | knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle |
| 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 | SpatialExperimentIO_0.99.7.tar.gz |
| Windows Binary (x86_64) | SpatialExperimentIO_0.99.7.zip |
| macOS Binary (x86_64) | SpatialExperimentIO_0.99.7.tgz |
| macOS Binary (arm64) | SpatialExperimentIO_0.99.7.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SpatialExperimentIO |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SpatialExperimentIO |
| Bioc Package Browser | https://code.bioconductor.org/browse/SpatialExperimentIO/ |
| Package Short Url | https://bioconductor.org/packages/SpatialExperimentIO/ |
| Package Downloads Report | Download Stats |