Events

January 30, 2023
  • Lambda Moses - “From geospatial to spatial -omics with SpatialFeatureExperiment and Voyager”

    January 30, 2023  4:00 pm - 5:00 pm
    https://partners.zoom.us/j/82826415806

    Zoom: https://partners.zoom.us/j/82826415806

    BWH Department ofComputational Pathology presents:

    2022-23 Junior InvestigatorsAdvanced Biomedical Computation (ABC) Seminar Series

    “Fromgeospatial to spatial -omics with SpatialFeatureExperiment and Voyager”

    Lambda Moses

    Graduate Student, Pachter Lab

    Division of Biology andBiological Engineering

    California Institute ofTechnology, Pasadena, CA, USA

    Monday January 30, 2023

    4:00-5:00pm 

    Zoom: https://partners.zoom.us/j/82826415806

    Abstract

    Spatiallocalization of gene expression and histological images in spatialtranscriptomics present many opportunities unavailable to non-spatial singlecell RNA-seq (scRNA-seq). There has been decades of research in spatial dataanalysis prior to the rise of spatial transcriptomics, mostly in geographicalspace. Some existing data analysis packages for spatial transcriptomics havebeen inspired by this tradition, such as Moran's I, Ripley's K, and Gaussianprocess regression. To bring more of the geospatial tradition to spatial-omics, we developed SpatialFeatureExperiment (SFE), which extends the existingBioconductor data structures SingleCellExperiment (SCE) and SpatialExperiment(SPE) with Simple Features to represent the geometries of Visium spots and cellsegmentation and perform geometric operations. We developed the Voyager packagethat performs exploratory spatial data analysis (ESDA) on SFE objects.Currently Voyager utilizes univariate global and local geospatial statistics,such as Moran's I, Geary's C, Moran plot, correlogram, local Moran, Getis-OrdGi*, and local spatial heteroscedasticity. Voyager also implements plottingfunctions for SFE objects and for the spatial analysis results. We plan to addbivariate and multivariate ESDA methods for the next Bioconductor release.

    SFE package: https://bioconductor.org/packages/release/bioc/html/SpatialFeatureExperiment.html
    Voyager package: https://bioconductor.org/packages/release/bioc/html/Voyager.html
    SFEData package, with example datasets for Voyager in the SFE format fromVisium, Slide-seq, CosMX, Xenium, and MERFISH: https://bioconductor.org/packages/release/data/experiment/html/SFEData.html
    Voyager documentation and vignettes: https://pachterlab.github.io/voyager/index.html
    Museum of Spatial Transcriptomics: https://pachterlab.github.io/LP_2021/index.html

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