SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor
Lukas M Weber,
Helena L Crowell,
Aaron TL Lun,
Stephanie C Hicks,
Posted 27 Jan 2021
bioRxiv DOI: 10.1101/2021.01.27.428431
Posted 27 Jan 2021
Summary: SpatialExperiment is a new data infrastructure for storing and accessing spatially resolved transcriptomics data, implemented within the R/Bioconductor framework, which provides advantages of modularity, interoperability, standardized operations, and comprehensive documentation. Here, we demonstrate the structure and user interface with examples from the 10x Genomics Visium and seqFISH platforms, and provide access to example datasets and visualization tools in the STexampleData, TENxVisiumData, and ggspavis packages. Availability and Implementation: The SpatialExperiment, STexampleData, and TENxVisiumData packages are available from Bioconductor. The package versions described in this manuscript are available in Bioconductor version 3.14 onwards. The ggspavis package is available from GitHub and has been submitted to Bioconductor. Contact: email@example.com, firstname.lastname@example.org Supplementary Information: Supplementary Tables and Figures are available online.
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