Analyzing GeoMx-NGS RNA Expression Data with GeomxTools
Introduction | Motivation & Scope | Getting started | Loading Data | Study Design | Modules Used | Sample Overview | QC & Pre-processing | Segment QC | Select Segment QC | Visualize Segment QC | Remove flagged segments | Probe QC | Set Probe QC Flags | Exclude Outlier Probes | Create Gene-level Count Data | Limit of Quantification | Filtering | Segment Gene Detection | Gene Detection Rate | Gene Filtering | Normalization | Unsupervised Analysis | UMAP & t-SNE | Clustering high CV Genes | Differential Expression | Within Slide Analysis: Glomeruli vs Tubules | Interpreting the results table | Between Slide Analysis: Diabetic Kidney Disease vs Healthy | Visualizing DE Genes | Volcano Plots | Plotting Genes of Interest | Heatmap of Significant Genes | Additional Resources | GeoMxSet Object Overview | Links & References | Additional Analysis Methods | MA Plot | Session Information
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