Introduction | What are Marker Genes? | How can we select marker genes? | The Mean Ratio Method | Goals of this Vignette | 1. Install and load required packages | Install DeconvoBuddies | Load Other Packages | 2. Download DLPFC snRNA-seq data. | 3. Find MeanRatio marker genes | 4. 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. Visualize Marker Genes Expression | Summary | Reproducibility | Bibliography

Introduction | What is Deconvolution? | Deconvolution Methods | Goals of this Vignette | Video Tutorial | Basics | 1. 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. How to run deconvolution with hspe | Conclusion | Reproducibility | Bibliography

Introduction | Basics | Install DeconvoBuddies | Required knowledge | Asking for help | Citing DeconvoBuddies | Quick start to using DeconvoBuddies | Access Data | Access and snRNA-seq example data | Explore snRNA-seq data in sce_DLPFC_example | Access Bulk RNA-seq data | Explore bulk data in rse_gene | Plotting Tools | Creating A Cell Type Color palette | Preview "classic" colors | Preview "gg" colors | Preview "tableau" colors | Check the color hex codes for "tableau" | Provide a palette from RColorBrewer | Plot Expression of Top Markers | plot expression of the top 6 Astro marker genes | Reproducibility | Bibliography

Basics | Install TREG | Required knowledge | Asking for help | Citing TREG | Overview | Why are TREGs useful? | What makes a gene a good TREG? | How to find candidate TREGs with TREG | Example TREG Application | Load Packages | Download and Prep Data | Filter and Refine to Cell Types of Interest | Filter Genes | Filter to Top 50% Expression | Calculate Proportion Zero and Pick Cutoff | Filter by the Max Proportion Zero | Run Rank Invariance | Selecting thresholds | Conclusion | Reproducibility | Bibliography