2023-08-02_spatialLIBD_BioC2023_demo

Transcript

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
   

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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:
   

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

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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)
   

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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()
   

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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
   

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7. Spatial Data Visualization
   vis_gene()
   vis_clus()
   

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

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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
   

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10. Spatial Domain Marker Finding
    registration_wrapper()
    

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

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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
    

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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
    

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14. lcolladotor.github.io
    @lcolladotor
    

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