SpatialExperiment

"SpatialExperiment" is a new infrastructure designed for storing and handling spatially resolved transcriptomics data. Implemented within the R/Bioconductor framework, this tool offers advantages such as modularity, interoperability, standardized operations, and comprehensive documentation. The package is demonstrated using examples from the 10x Genomics Visium and seqFISH platforms. Users can also access example datasets and visualization tools through associated packages like STexampleData, TENxVisiumData, and ggspavis.

Topic

Transcriptomics;Proteomics;Workflows;Epigenomics

Detail

  • Operation: Data retrieval;Visualisation

  • Software interface: Library,Command-line tool

  • Language: R

  • License: The GNU General Public License v3.0

  • Cost: Free

  • Version name: 1.12.0

  • Credit: The Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation, National Institutes of Health/NIMH, ‘Programma per Giovani Ricercatori Rita Levi Montalcini’ granted by the Italian Ministry of Education, University, the National Cancer Institute of the National Institutes of Health, Royal Society Newton International Fellowship.

  • Input: -

  • Output: -

  • Contact: Dario Righelli dario.righelli@gmail.com

  • Collection: -

  • Maturity: Stable

Publications

  • SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor
  • Righelli D, Weber LM, Crowell HL, Pardo B, Collado-Torres L, Ghazanfar S, Lun ATL, Hicks SC, Risso D. SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor. Bioinformatics. 2022 May 26;38(11):3128-3131. doi: 10.1093/bioinformatics/btac299. PMID: 35482478; PMCID: PMC9154247.
  • https://doi.org/10.1093/bioinformatics/btac299
  • PMID: 35482478
  • PMC: PMC9154247

Download and documentation

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