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.
SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor / Righelli, Dario; Weber, Lukas M; Crowell, Helena L; Pardo, Brenda; Collado-Torres, Leonardo; Ghazanfar, Shila; Lun, Aaron T L; Hicks, Stephanie C; Risso, Davide. - In: BIOINFORMATICS. - ISSN 1367-4803. - 38:11(2022), pp. 3128-3131. [10.1093/bioinformatics/btac299]
SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor
Righelli, Dario;
2022
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.| File | Dimensione | Formato | |
|---|---|---|---|
|
Righelli2021preprint.pdf
non disponibili
Licenza:
Non specificato
Dimensione
326.11 kB
Formato
Adobe PDF
|
326.11 kB | Adobe PDF | Visualizza/Apri Richiedi una copia |
|
btac299 (1).pdf
non disponibili
Licenza:
Non specificato
Dimensione
706.22 kB
Formato
Adobe PDF
|
706.22 kB | Adobe PDF | Visualizza/Apri Richiedi una copia |
I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
