/usr/lib/R/site-library/Mergeomics/INDEX is in r-bioc-mergeomics 1.6.0-1.
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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
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