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spammR: an R package designed for analysis and integration of spatial multi-omic measurements.

Yannick Mahlich1, Harkirat Sohi1, Marija Veličković2

  • 1Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.

Bioinformatics Advances
|June 29, 2026
PubMed
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This study introduces spammR, an R package for analyzing spatial multi-omics data, particularly from mass spectrometry. It facilitates integrating diverse omics data types within a single tissue sample.

Area of Science:

  • Biotechnology
  • Bioinformatics
  • Computational Biology

Background:

  • Spatial omics technologies rapidly advance, enabling high-resolution measurement of transcripts, proteins, and metabolites.
  • Current analytical tools primarily support spatial transcriptomics, limiting broader multi-omics integration.
  • Analyzing diverse spatial omics data, like mass spectrometry, requires specialized computational approaches.

Purpose of the Study:

  • To present spammR, an R package designed for the end-to-end analysis of spatial multi-omics data.
  • To specifically address the integration of mass spectrometry-derived spatial omics datasets.
  • To enable cross-platform analysis of multiple data types (e.g., sequencing, metabolites, proteins) within the same tissue.

Main Methods:

  • Development of an R package named spammR (spatial analysis of multi-omics measurements in R).

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  • Implementation focused on integrating diverse omics data types from spatial measurements.
  • Package designed for analysis of mass spectrometry-derived spatial omics data.

    • Main Results:

    • spammR provides end-to-end analysis capabilities for spatial multi-omics data.
    • The package facilitates the integration of various data types, including mass spectrometry, sequencing, and protein data.
    • Enables analysis of multi-omics data within a spatial context.

    Conclusions:

    • spammR enhances the analysis of spatial multi-omics data, particularly for mass spectrometry.
    • The R package promotes integrated analysis across different omics modalities within tissues.
    • spammR is available via GitHub for the research community.