EXTID2NAME              EXTID2NAME
aggregate_enrichment    Aggregate multiple enrichment results (Late
                        Fusion)
aggregate_omics         Aggregate multi-omics gene/protein-level
                        statistics
bayes_enrich            Bayesian term selection for enrichment results
bayes_summary           Summarize Bayesian enrichment results
classify_omics_pattern
                        Classify pathway-level multi-omics patterns
collapse_multilayer_scores
                        Collapse multi-layer diffusion scores
compareClusterResult-class
                        Class "compareClusterResult" This class
                        represents the comparison result of gene
                        clusters by GO categories at specific level or
                        GO enrichment analysis.
enrichResult-class      Class "enrichResult" This class represents the
                        result of enrichment analysis.
enrichit_params         Common parameters for enrichit functions
extract_mnsea_subnetwork
                        Extract pathway subnetwork data from a
                        'mnseaResult'
geneID                  geneID generic
geneInCategory          geneInCategory generic
get_mnsea_contribution
                        Get cached contribution tables from a
                        'mnseaResult'
get_omics_contribution
                        Get gene-level omics contribution for a
                        specific pathway
gsea                    Gene Set Enrichment Analysis (GSEA)
gseaResult-class        Class "gseaResult" This class represents the
                        result of GSEA analysis
gseaScores              Calculate GSEA Running Enrichment Scores
gsea_gson               gsea_gson
gsfilter                gsfilter
harmonize_ids           Harmonize feature IDs to a target space
mnsea                   Multi-layer Network-based Gene Set Enrichment
                        Analysis
mnseaResult-class       Class "mnseaResult" This class represents the
                        result of multi-layer Network-based Set
                        Enrichment Analysis.
mnsea_gson              Multi-layer NSEA using a GSON object
nsea                    Network-based Gene Set Enrichment Analysis
nseaResult-class        Class "nseaResult" This class represents the
                        result of Network-based Set Enrichment Analysis
                        (NSEA).
nsea_gson               Network-based GSEA using a GSON object
ora                     Over-Representation Analysis (ORA)
ora_gson                ora-gson
prepare_multilayer_network
                        Prepare multi-layer network for repeated
                        propagation
prepare_network         Prepare network for repeated NSEA runs
propagate_multilayer    Propagate signals on a multi-layer network
select_features_for_ora
                        Select features for ORA
setReadable             setReadable
show                    show method
summary                 summary method
