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Install and load required packages", "Install DeconvoBuddies", "Load Other Packages", "2. Download DLPFC RNA-seq data, and reference snRNA-seq data.", "Bulk RNA-seq data", "Reference snRNA-seq data", "Orthogonal Cell Type Proportion from RNAScope/IF", "3. Select Marker Genes", "Use get_mean_ratio() to find marker genes.", "Plot the top marker genes", "Create a List of Marker Genes", "4. Prep Data and Run Bisque", "Prepare data", "Run Bisque", "Explore Output", "5. Explore deconvolution output and create composition plots with DeconvoBuddies tools", "6. Check proportion against RNAScope/IF estimated proportions", "7. 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Find 1vALL marker genes", "Run 1vALL DE to find markers for each cell type - takes 5min+", "marker_stats_1vAll <- findMarkers_1vAll(", "sce = sce, # sce is the SingleCellExperiment with our data", "assay_name = \"counts\",", "cellType_col = \"cellType_broad_hc\", # column in colData with cell type info", "mod = \"~BrNum\" # Control for donor stored in \"BrNum\" with mod", "raw_logFC = TRUE # also retain raw logFC in addition to standardized", ")", "load 1vAll data to save time, data is equivalent to the above code", "5. Compare Marker Gene Selection", "Hockey Stick Plots", "6. 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