SpatialExperimentIO
Read in Xenium, CosMx, MERSCOPE or STARmapPLUS data as SpatialExperiment object
Bioconductor version: 3.23 · Package version: 1.4.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SpatialExperimentIO")Details
| Maintainer | Yixing E. Dong <estelladong729@gmail.com> |
| Author | Yixing E. Dong [aut, cre] (ORCID: <https://orcid.org/0009-0003-5115-5686>) |
| License | Artistic-2.0 |
| URL | https://github.com/estellad/SpatialExperimentIO |
| Bug Reports | https://github.com/estellad/SpatialExperimentIO/issues |
| Downloads rank | 238 |
| Source branch | RELEASE_3_23 |
| biocViews | DataImport, DataRepresentation, GeneExpression, Infrastructure, SingleCell, Software, Spatial, Transcriptomics |
Documentation
Download
Dependencies
Depends: R (>= 4.1.0)
Imports: DropletUtils, SpatialExperiment, SingleCellExperiment, methods, data.table, arrow, purrr, S4Vectors
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle