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Thinking Spatially: Using spatial transcriptomic tools from LIBD

Thinking Spatially: Using spatial transcriptomic tools from LIBD

Slides from Computational Biology Club at UCL Child Health May 24th 2023

Goals of the workshop:
Access Data from the spatialLIBD
Understand the SpatialExperiment data structure
Visualize continuous and discrete variables in spatial Data
Use spatialLIBD registration tools for marker finding
Complete spatial registration on an example data set

Louise Huuki-Myers

May 24, 2023
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  1. Thinking Spatially
    Using spatial transcriptomic tools from the
    Lieber Institute for Brain Development
    Louise Huuki-Myers
    Staff Scientist
    @lahuuki
    lahuuki.github.io
    Download these slides: speakerdeck.com/lahuuki

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  2. About LIBD
    Lieber Institute for Brain Development
    ● Non-profit Research Institute in Baltimore, MD
    ● Study the genetics of neuropsychiatric disorders 🧬
    ● 139 multidisciplinary scientists
    ● Affiliated with the Johns Hopkins Medical School
    2
    Baltimore
    Maryland 🔸

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  3. Our R/Bioconductor Powered Data Science Team
    ● Led by Leonardo Collado-Torres
    ● Computational lab specializing in:
    ○ RNA seq analysis
    ■ Bulk, single cell, spatial
    ○ Open Source software development
    ○ Knowledge sharing
    ■ Data Science Guidance Sessions
    ■ Rstat Club: Videos available
    www.youtube.com/@lcolladotor
    ● Team website
    ○ lcolladotor.github.io/
    3

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  4. Goals for this workshop
    1. Access Data from the spatialLIBD
    2. Understand the SpatialExperiment data structure
    3. Visualize continuous and discrete variables in spatial
    Data
    4. Use spatialLIBD registration tools for marker
    finding
    5. Complete spatial registration on an example data set

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

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  6. SpatialLIBD & spatialDLPFC Datasets
    research.libd.org/spatialLIBD/
    LieberInstitute/spatialDLPFC

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  7. 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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  8. Spatial Experiment
    bioconductor.org/packages/release/bioc/vignettes/SpatialExperiment/inst/doc/S
    patialExperiment.html

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  9. Spatial Data Visualization
    vis_gene()
    vis_clus()

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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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