Complete RNA-seq Analysis Workflow with VISTA
Introduction | What is VISTA? | Dataset Overview | Installation and Setup | Data Preparation | Load the airway dataset | Extract counts and metadata | Prepare data for VISTA | Create VISTA Object | Using DESeq2 backend | Validate object integrity | Alternative: Using edgeR backend | Alternative: Using limma-voom backend | Advanced: covariates, design formula, and consensus mode | Add gene annotations | Explore the Results | Access differential expression results | Count significant genes | Quality Control Visualizations | Sample Correlation Heatmap | Basic correlation heatmap | Customize color scheme | Show correlation values | Principal Component Analysis (PCA) | Basic PCA with labels | PCA colored by different metadata | PCA with top variable genes | PCA with custom circle size | PCA without labels | Multidimensional Scaling (MDS) | Basic MDS plot | MDS with top variable genes | MDS with custom shapes | Uniform Manifold Approximation and Projection (UMAP) | Basic UMAP plot | UMAP colored by a user-defined metadata column | Differential Expression Visualizations | DEG Count Summary | Basic count barplot | Faceted by regulation | Volcano Plot | Basic volcano plot | Customize cutoffs and labels | Custom colors | MA Plot | Basic MA plot | Label top genes | Custom cutoffs | Expression Pattern Analysis | Prepare gene sets | Expression Heatmaps | Basic heatmap | Heatmap with explicit gene set | Heatmap with k-means clustering | Heatmap with column annotations | Heatmap with multiple column annotations and cluster_by | Heatmap showing each replicate | Expression Barplots | Basic barplot | Log-transformed with statistics | Per-sample barplot for selected genes | Compare up and down regulated genes | Expression Boxplots | Basic boxplot | Boxplot without faceting | Boxplot with faceting by gene | Boxplot with gene facets AND statistics | Pooled genes with statistics | Log-transformed with p-values | Expression Violin Plots | Basic violin plot | Violin with log2 transformation | Violin with z-score transformation | Additional Expression Plots | Density plot | Scatter plot (sample vs sample) | Line plot (expression across samples) | Lollipop plot | Per-sample lollipop plot | Joyplot by treatment group | Joyplot by sample | Raincloud plot (expression) | Functional Enrichment Analysis | MSigDB Enrichment | Hallmark gene sets - Upregulated | Hallmark gene sets - Downregulated | Enrichment Visualizations | VISTA dotplot (default) | Barplot (clusterProfiler native) | Dotplot with customization | Network plot (clusterProfiler native) | Chord diagram (gene--pathway relationships) | Pathway-Specific Expression Heatmaps | Extract genes from top pathways | Heatmap of genes from top enriched pathways | GO Enrichment | Biological Process | GO Visualization | Gene Set Enrichment Analysis (GSEA) | GSEA with MSigDB Hallmark gene sets | GSEA with GO Biological Process | GSEA enrichment overview | GSEA plot for top pathway | GSEA plot for multiple pathways | GSEA with GO visualization | KEGG Pathway Enrichment | KEGG upregulated genes | KEGG downregulated genes | KEGG Visualization | Fold-Change Analysis | Fold-change Matrix | Fold-change Barplot and Lollipop | Per-gene fold-change barplot | Per-gene fold-change lollipop | Fold-change Raincloud | Fold-change Heatmap | Basic FC heatmap | FC heatmap for selected genes | FC heatmap with gene names | FC heatmap for specific gene set | Export Results | Export DE results to file | Save VISTA object | Summary | Workflow Completed | Key Features Demonstrated | Plotting Functions Used | QC Plots | DE Visualization | Expression Plots | Enrichment Plots | Fold-Change | Next Steps | Session Information | References
Rendered fromVISTA-airway.Rmdusingknitr::rmarkdown