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

Transcript

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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