adjMatToElist           converts adjacency matrix to edge list
alpaca                  Main ALPACA function
alpacaCommunityStructureRotation
                        Comparing node community membership between two
                        networks
alpacaComputeDWBMmatmScale
                        Differential modularity matrix
alpacaComputeDifferentialScoreFromDWBM
                        Compute Differential modularity score from
                        differential modularity matrix
alpacaComputeWBMmat     Compute modularity matrix for weighted
                        bipartite network
alpacaCrane             Find the robust nodes in ALPACA community using
                        CRANE
alpacaDeltaZAnalysis    Edge subtraction method (CONDOR optimizaton)
alpacaDeltaZAnalysisLouvain
                        Edge subtraction method (Louvain optimizaton)
alpacaExtractTopGenes   Extract core target genes in differential
                        modules
alpacaGOtabtogenes      The top GO term associated genes in each module
alpacaGenLouvain        Generalized Louvain optimization
alpacaGetMember         get the member vector from alpaca object
alpacaGoToGenes         Map GO terms to gene symbols
alpacaListToGo          GO term enrichment for a list of gene sets
alpacaMetaNetwork       Create alpacaMetaNetwork for Louvain
                        optimization
alpacaNodeToGene        Remove tags from gene names
alpacaObjectToDfList    Converts alpaca output into list of data frames
alpacaRotationAnalysis
                        Community comparison method (CONDOR
                        optimizaton)
alpacaRotationAnalysisLouvain
                        Community comparison method (CONDOR
                        optimizaton)
alpacaSimulateNetwork   Simulated networks
alpacaTestNodeRank      Enrichment in ranked list
alpacaTidyConfig        Renumbering community membership vector
alpacaTopEnsembltoTopSym
                        Translating gene identifiers to gene symbols
alpacaWBMlouvain        Generalized Louvain method for bipartite
                        networks
condorCluster           Main clustering function for condor.
condorCoreEnrich        Compare qscore distribution of a subset of
                        nodes to all other nodes.
condorCreateObject      creates condor object
condorMatrixModularity
                        Iteratively maximize bipartite modularity.
condorModularityMax     Iteratively maximize bipartite modularity.
condorPlotCommunities   Plot adjacency matrix with links grouped and
                        colored by community
condorPlotHeatmap       Plot weighted adjacency matrix with links
                        grouped by community
condorQscore            Calculate Qscore for all nodes
condorRun               Run CONDOR clustering
craneBipartite          Pertrubs the bipartite network with fixed node
                        strength
craneUnipartite         Pertrubs the unipartite network with fixed node
                        strength from adjacency matrix
createCondorObject      Create list amenable to analysis using 'condor'
                        package.
createPandaStyle        Create a Cytoscape visual style for PANDA
                        network
elistAddTags            Adds "_A" to first column and "_B" to second
                        column
elistIsEdgeOrderEqual   check if first two columns are identical
elistRemoveTags         undo elistAddTags
elistSort               Sorts the edge list based on first two columns
                        in alphabetical order
elistToAdjMat           Converts edge list to adjacency matrix
exon.size               Gene length
genes                   Example of a gene list
isElist                 Check if data frame is an edge list
jutterDegree            CRANE Beta perturbation function. This function
                        will add noice to the node strength sequence.
lioness                 Compute LIONESS (Linear Interpolation to Obtain
                        Network Estimates for Single Samples)
lionessPy               Run python implementation of LIONESS
monster                 MOdeling Network State Transitions from
                        Expression and Regulatory data (MONSTER)
monsterBereFull         Bipartite Edge Reconstruction from Expression
                        data (composite method with direct/indirect)
monsterCalculateTmPValues
                        Calculate p-values for a tranformation matrix
monsterCheckDataType    Checks that data is something MONSTER can
                        handle
monsterGetTm            monsterGetTm
monsterHclHeatmapPlot   Transformation matrix plot
monsterMonsterNI        Bipartite Edge Reconstruction from Expression
                        data
monsterPlotMonsterAnalysis
                        monsterPlotMonsterAnalysis
monsterPrintMonsterAnalysis
                        monsterPrintMonsterAnalysis
monsterRes              MONSTER results from example cell-cycle yeast
                        transition
monsterTransformationMatrix
                        Bi-partite network analysis tools
monsterTransitionNetworkPlot
                        This function uses igraph to plot the
                        transition matrix (directed graph) as a
                        network. The edges in the network should be
                        read as A 'positively/negatively contributes
                        to' the targeting of B in the target state.
monsterTransitionPCAPlot
                        Principal Components plot of transformation
                        matrix
monsterdTFIPlot         This function plots the Off diagonal mass of an
                        observed Transition Matrix compared to a set of
                        null TMs
mut.ucec                Example of mutation data
otter                   Run OTTER in R
pandaPy                 Run Python implementation PANDA in R
pandaToAlpaca           Use two PANDA network to generate an ALPACA
                        result
pandaToCondorObject     Turn PANDA network into a CONDOR object
runEgret                Run EGRET in R
sambar                  Main SAMBAR function.
sambarConvertgmt        Convert .gmt files into a binary matrix.
sambarCorgenelength     Normalize gene mutation scores by gene length.
sambarDesparsify        De-sparsify gene-level mutation scores into
                        gene set-level mutation scores.
small1976               Pollinator-plant interactions
sourcePPI               Source the Protein-Protein interaction in
                        STRING database
visPandaInCytoscape     Plot PANDA network in Cytoscape
yeast                   Toy data derived from three gene expression
                        datasets and a mapping from transcription
                        factors to genes.
