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2023-08-02_spatialLIBD_BioC2023_demo

 2023-08-02_spatialLIBD_BioC2023_demo

Leonardo Collado-Torres

July 24, 2023
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  1. BioC2023 Package Demo
    Analyzing Spatially-Resolved Transcriptomics
    Data from Visium using spatialLIBD
    Louise Huuki-Myers Leonardo Collado Torres
    Staff Scientist Investigator
    @lahuuki
    lahuuki.github.io
    Download these slides: speakerdeck.com/lcolladotor
    lcolladotor.github.io
    @lcolladotor
    August 2, 2023

    View Slide

  2. Goals for this package demo
    1. Access Data from the spatialLIBD
    2. Understand the SpatialExperiment data structure
    3. Visualize continuous and discrete variables in spatial
    Data
    4. Gene set enrichment analysis
    5. Use spatialLIBD registration tools for marker
    finding
    6. Complete spatial registration on an example data set
    Slides:

    View Slide

  3. Background Spatial Transcriptomics
    Image Credit: 10x Genomics
    Histology
    Neurons in GM White Matter Histological Layer
    5
    3
    Slides:

    View Slide

  4. #spatialDLPFC
    4
    doi.org/10.1101/2023.02.15.528722
    research.libd.org/spatialDLFPC/
    Louise A
    Huuki-Myers
    @lahuuki
    Abby Spangler
    @abspangler
    Nicholas J Eagles
    @Nick-Eagles
    (GitHub)

    View Slide

  5. name class size nrow ncol length
    sce SingleCellExperiment 2.08 33538 47681 NA
    sce_layer SingleCellExperiment 0.03 22331 76 NA
    sce_example SingleCellExperiment 0.10 33538 47681 NA
    spatialDLPFC_snRNAseq SingleCellExperiment - - - -
    spe SpatialExperiment 2.04 33538 47681 NA
    spatialDLPFC_Visium SpatialExperiment 6.97 28916 113927 NA
    spatialDLPFC_Visium_pseudobulk SpatialExperiment 0.06 12225 268 NA
    spatialDLPFC_Visium_SPG SpatialExperiment 0.82 27722 15113 NA
    Visium_SPG_AD_Visium_wholegenome_spe SpatialExperiment 2.29 27853 38115 NA
    Visium_SPG_AD_Visium_targeted_spe SpatialExperiment 1.57 23485 38115 NA
    Visium_SPG_AD_Visium_wholegenome_pseudobulk_spe SpatialExperiment 0.01 8443 41 NA
    modeling_results list 0.02 NA NA 3
    spatialDLPFC_Visium_modeling_results list 0.02 NA NA 3
    Visium_SPG_AD_Visium_wholegenome_modeling_results list 0.01 NA NA 3
    Access these Datasets with
    spatialLIBD::fetch_data()

    View Slide

  6. 6
    SpatialExperiment: infrastructure for spatially resolved
    transcriptomics data in R using Bioconductor
    Righelli, Weber, Crowell, et al, Bioinformatics, 2022
    DOI 10.1093/bioinformatics/btac299
    Dario Righellli Helena L Crowell
    @drighelli @CrowellHL
    Lukas M Weber
    @lmwebr

    View Slide

  7. Spatial Data Visualization
    vis_gene()
    vis_clus()

    View Slide

  8. Gene set enrichment
    KR Maynard, L Collado-Torres, et al, Nature Neuroscience, 2021 10.1038/s41593-020-00787-0

    View Slide

  9. Live code
    ● pkgdown documentation website
    ○ http://research.libd.org/spatialLIBD/
    ● spatialLIBD::fetch_data("spatialDLPFC_Visium")
    ○ http://research.libd.org/spatialLIBD/reference/fetch_data.html
    ● spatialLIBD::vis_gene() example
    ○ http://research.libd.org/spatialLIBD/reference/vis_gene.html
    ● shiny app using spatialDLPFC data
    ○ http://research.libd.org/spatialLIBD/reference/run_app.html
    ● gene_set_enrichment() + gene_set_enrichment_plot()
    ○ http://research.libd.org/spatialLIBD/reference/gene_set_enrichment.html +
    http://research.libd.org/spatialLIBD/reference/gene_set_enrichment_plot.html

    View Slide

  10. Spatial Domain Marker Finding
    registration_wrapper()

    View Slide

  11. Spatial Registration
    https://research.libd.org/spatialLIBD/articles/guide_to_spatial_registration.html

    View Slide

  12. Live Code
    ● spatialLIBD::registration_wrapper()
    ○ https://research.libd.org/spatialLIBD/reference/registration_wrapper.html
    ● spatialLIBD::layer_stat_cor()
    ○ https://research.libd.org/spatialLIBD/reference/layer_stat_cor.html
    ● spatialLIBD::layer_stat_cor_plot()
    ○ https://research.libd.org/spatialLIBD/reference/layer_stat_cor_plot.html
    Vignette:
    https://research.libd.org/spatialLIBD/articles/guide_to_spatial_registration.html

    View Slide

  13. @MadhaviTippani
    Madhavi Tippani
    @HeenaDivecha
    Heena R Divecha
    @lmwebr
    Lukas M Weber
    @stephaniehicks
    Stephanie C Hicks
    @abspangler
    Abby Spangler
    @martinowk
    Keri Martinowich
    @CerceoPage
    Stephanie C Page
    @kr_maynard
    Kristen R Maynard
    @lcolladotor
    Leonardo Collado-Torres
    @Nick-Eagles (GH)
    Nicholas J Eagles
    Kelsey D Montgomery
    Sang Ho Kwon
    Image Analysis
    Expression Analysis
    Data Generation
    Thomas M Hyde
    @lahuuki
    Louise A Huuki-Myers
    @BoyiGuo
    Boyi Guo
    @mattntran
    Matthew N Tran
    @sowmyapartybun
    Sowmya Parthiban
    Slides available at
    speakerdeck.com
    /lcolladotor
    + Many more LIBD, JHU, and
    external collaborators
    @mgrantpeters
    Melissa Grant-Peters
    @prashanthi-ravichandran (GH)
    Prashanthi Ravichandran

    View Slide

  14. lcolladotor.github.io
    @lcolladotor

    View Slide