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

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:

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

#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)

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()

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

Spatial Data Visualization vis_gene() vis_clus()

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

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

Spatial Domain Marker Finding registration_wrapper()

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

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

@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

lcolladotor.github.io @lcolladotor