Dario Righelli1, Lukas M Weber2, Helena L Crowell3,4, Brenda Pardo5,6, Leonardo Collado-Torres6, Shila Ghazanfar7, Aaron T L Lun8, Stephanie C Hicks2, Davide Risso1. 1. Department of Statistical Sciences, University of Padova, Padova, Italy. 2. Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA. 3. Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland. 4. SIB Swiss Institute of Bioinformatics, Zurich, Switzerland. 5. Escuela Nacional de Estudios Superiores Unidad Juriquilla, Universidad Nacional Autónoma de México, Queretaro, Mexico. 6. Lieber Institute for Brain Development, Baltimore, MD, USA. 7. Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom. 8. Genentech, South San Francisco, CA, USA.
Abstract
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, TENxVisiumData, and ggspavis packages are available from Bioconductor. The package versions described in this manuscript are available in Bioconductor version 3.15 onwards. SUPPLEMENTARY INFORMATION: Supplementary tables and figures are available at Bioinformatics online.
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, TENxVisiumData, and ggspavis packages are available from Bioconductor. The package versions described in this manuscript are available in Bioconductor version 3.15 onwards. SUPPLEMENTARY INFORMATION: Supplementary tables and figures are available at Bioinformatics online.
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