MSEA.KDA.onestep        Run MSEA and/or KDA in one step
Mergeomics-package      Integrative network analysis of omics data
job.kda                 Key Driver Analyzing results
kda.analyze             Weighted key driver analysis (wKDA) main
                        function
kda.analyze.exec        Auxiliary function for weight key driver
                        analysis (wKDA)
kda.analyze.simulate    Weighted key driver analysis (wKDA) simulation
kda.analyze.test        Calculate enrichment score for wKDA
kda.configure           Set parameters for weighted key driver analysis
                        (wKDA)
kda.finish              Organize and save results
kda.finish.estimate     Estimate measures for accomplished wKDA results
kda.finish.save         Save full wKDA results
kda.finish.summarize    Summarize the wKDA results
kda.finish.trim         Trim numbers before save
kda.prepare             Prepare graph topology for weighted key driver
                        analysis
kda.prepare.overlap     Extract overlapping co-hubs
kda.prepare.screen      Prepare hubs and hubnets
kda.start               Import data for weighted key driver analysis
kda.start.edges         Import nodes and edges of graph topology
kda.start.identify      Convert identities to indices for wKDA
kda.start.modules       Import module descriptions
kda2cytoscape           Generate input files for Cytoscape
kda2cytoscape.colorize
                        Trace module memberships of genes
kda2cytoscape.colormap
                        Assign one color to each unique module
kda2cytoscape.drivers   Select top key drivers for each module
kda2cytoscape.edges     Find edges of a given node with a specified
                        depth
kda2cytoscape.exec      Evaluate each module separately for
                        visualization
kda2cytoscape.identify
                        Match identities with respect to given variable
                        name
kda2himmeli             Generate input files for Himmeli
kda2himmeli.colorize    Trace module memberships of genes
kda2himmeli.colormap    Assign one color to each unique module
kda2himmeli.drivers     Select top key drivers for each module
kda2himmeli.edges       Find edges of a given node with a specified
                        depth
kda2himmeli.exec        Evaluate each module separately for
                        visualization
kda2himmeli.identify    Match identities with respect to given variable
                        name
ssea.analyze            Marker set enrichment analysis (MSEA)
ssea.analyze.observe    Collect enrichment score statistics for MSEA
ssea.analyze.randgenes
                        Estimate enrichment from randomized genes
ssea.analyze.randloci   Estimate enrichment from randomized marker
ssea.analyze.simulate   Simulate scores for MSEA
ssea.analyze.statistic
                        MSEA statistics for enrichment score
ssea.control            Add internal positive control modules for MSEA
ssea.finish             Organize and save MSEA results
ssea.finish.details     Organize and save module, gene, top locus, Ps
                        of MSEA results
ssea.finish.fdr         Organize and save FDR results of the MSEA
ssea.finish.genes       Organize and save gene-realted MSEA results
ssea.meta               Merge multiple MSEA results into meta MSEA
ssea.prepare            Prepare an indexed database for MSEA
ssea.prepare.counts     Calculate hit counts up to a given quantile
ssea.prepare.structure
                        Construct hierarchical representation of
                        components
ssea.start              Create a job for MSEA
ssea.start.configure    Check parameters before MSEA
ssea.start.identify     Convert identities to indices for MSEA
ssea.start.relabel      Update gene symbols after merging overlapped
                        markers
ssea2kda                Generate inputs for wKDA
ssea2kda.analyze        Apply second MSEA after merging the modules
ssea2kda.import         Import genes and top markers from original
                        files
tool.aggregate          Aggregate the entries
tool.cluster            Hierarchical clustering of nodes
tool.cluster.static     Static hierarchical clustering
tool.coalesce           Calculate overlaps between groups (main
                        function)
tool.coalesce.exec      Find, merge, and trim overlapping clusters
tool.coalesce.find      Find overlapping clusters
tool.coalesce.merge     Merge overlapping clusters
tool.fdr                Estimate False Discovery Rates (FDR)
tool.fdr.bh             Benjamini and Hochberg False Discovery Rate
tool.fdr.empirical      Estimate Empirical False Discovery Rates
tool.graph              Convert an edge list to a graph representation
tool.graph.degree       Find degrees of the nodes
tool.graph.list         Return edge list for each node
tool.metap              Estimate meta P-values
tool.normalize          Estimate statistical scores based on Gauss
                        distribution
tool.normalize.quality
                        Check normalization quality
tool.overlap            Calculate overlaps between groups of specified
                        items
tool.read               Read a data frame from a file
tool.save               Save a data frame in tab-delimited file
tool.subgraph           Determine network neighbors for a set of nodes
tool.subgraph.find      Find edges to adjacent nodes
tool.subgraph.search    Search neighborhoods for given nodes
tool.subgraph.stats     Calculate node degrees and strengths
tool.translate          Translate gene symbols
tool.unify              Convert a distribution to uniform ranks
