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SpatialExperimentIO
This is thereleased version of SpatialExperimentIO; for the devel version, seeSpatialExperimentIO.
Read in Xenium, CosMx, MERSCOPE or STARmapPLUS data as SpatialExperiment object
Bioconductor version: Release (3.22)
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: 0009-0003-5115-5686
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")BiocManager::install("SpatialExperimentIO")For older versions of R, please refer to the appropriateBioconductor 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 | 1.2.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (0.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.1.0) |
| 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 | SpaceTrooper, OSTA |
| Suggests Me | OSTA.data |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | SpatialExperimentIO_1.2.0.tar.gz |
| Windows Binary (x86_64) | SpatialExperimentIO_1.2.0.zip (64-bit only) |
| macOS Binary (x86_64) | SpatialExperimentIO_1.2.0.tgz |
| macOS Binary (arm64) | SpatialExperimentIO_1.2.0.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 |