Multi-omics pathway enrichment analysis | Introduction | Pathway enrichment analysis using the ranked hypergeometric test | Using the package | Basic use | ActivePathways 2.0 Directional integration of multi-omics data | Directional data integration at the gene level | Constraints vector intuition | Pathway-level insight | Comparing standard and directional pathway analysis | Merging results for visualization in Cytoscape | Examining pathways affected by directional analysis | Significance threshold and returning all results | GMT objects | Background gene set for statistical analysis | Merging p-values | Cutoff for filtering the ranked gene list for pathway enrichment analysis | Adjusting P-values using multiple testing correction | The results table of ActivePathways | Writing results to a CSV file | Visualising pathway enrichment results using enrichment maps in Cytoscape | Creating enrichment maps using the ActivePathways results | Required software | Required files | Creating the enrichment map | Colour the nodes of the network to visualise supporting omics datasets | Visualizing directional impact with node borders | Alternative node coloring | References