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Exploring Giotto Suite for spatial transcriptom...

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Avatar for Nicholas Eagles Nicholas Eagles
October 09, 2024
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Exploring Giotto Suite for spatial transcriptomic analysis

I walk through the Giotto Suite preprint (https://doi.org/10.1101/2023.11.26.568752), which covers a family of R packages for spatial transcriptomics.

Avatar for Nicholas Eagles

Nicholas Eagles

October 09, 2024
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Transcript

  1. Giotto Suite: a multi-scale and technology-agnostic spatial multi-omics analysis ecosystem

    Chen et al. DOI: 10.1101/2023.11.26.568752 Presented by: Nick Eagles 2024/09/25

  2. giottoPoints giottoPolygon giottoLargeImage

  3. Fig S2C: Giotto object structure

  4. None

  5. Fig S5: segmentation at different spatial scales Cellular and nuclear

    segmentation of the same MERFISH data

  6. Fig S5: Differences in vs out of cells

  7. Fig S10: Multiomic Integration

  8. RNA Protein Multi-omic Deconvolved SC

  9. Fig S7: Comparison across technologies

  10. None
  11. None

  12. Miscellaneous Notes - On-disk representations using database backend for points

    and polygons (dbPointsProxy and dbPolygonProxy) - Expression matrices stored as HDF5Matrix objects - Conversion utilities with SpatialExperiment, AnnData, and Seurat objects