enrichment_chart(): Bubble Chart of Enrichment Results | visualize_terms(): Enriched Term Diagrams | term_gene_heatmap(): Terms by Genes Heatmap | create_term_gene_graph() & create_term_gene_plot: Term-Gene Graph | UpSet_plot(): UpSet Plots of Enriched Terms

Overview | Active-subnetwork-oriented Enrichment Analysis | Useful arguments | Filtering Input Genes | Output Directory | Gene Sets for Enrichment | Filtering Enriched Terms by Adjusted-p Values | Protein-protein Interaction Network | Active Subnetwork Search Method | Other Arguments | Output | Enriched Terms Data Frame | HTML Report (created when output_dir is set) | Enriched Term Diagrams | Clustering Enriched Terms | Hierarchical Clustering | Heuristic Fuzzy Multiple-linkage Partitioning | Aggregated Term Scores per Sample | Comparison of 2 pathfindR Results | Analysis with Custom Gene Sets

Get PIN File | Get Gene Sets List | KEGG Pathway Gene Sets | Reactome Pathway Gene Sets | MSigDB Gene Sets

Overview | Example Input | "Distance-based" Method | "RWR" Method

Preparation of Necessary Data | Obtain Organism-specific Gene Sets | Obtain Organism-specific Protein-protein Interaction Network | Running pathfindR on non-Homo sapiens data | Input Data | Executing run_pathfindR() | Built-in Mus musculus Data

Overview | Predicting Impact of Coding Variants | Driver Gene Prioritization - Personalized Analysis | Load the package and prepare input data | ANNOVAR CSV output | SCNA table | phenolyzer output | Create the features data frame | Prioritize cancer driver genes | Driver Gene Prioritization - Batch Analysis