.checkGTL               Check GeneTonic List format
.checkGenesets          Check genesets format
.checkPPI               Check PPI format
.checkScores            Check distance scores format
.filterGenesets         Filter Genesets from the input data
.findSeparator          Make an educated guess on the separator
                        character
.getClusterDatatable    Map each geneset to the cluster it belongs
.getGenesetDescriptions
                        Get gene set descriptions
.getNumberCores         Determine the number of cores to use for a
                        function
.graphMetricsGenesetsDT
                        Generate a 'data.frame' of graph metrics
.sepguesser             Make an educated guess on the separator
                        character
GeDi                    GeDi main function
buildClusterGraph       Build a cluster graph
buildGraph              Construct a graph
buildHistogramData      Prepare data for 'gsHistogram()'.
calculateJaccard        Calculate the Jaccard distance
calculateKappa          Calculate the Kappa distance
calculateSorensenDice   Calculate the Sorensen-Dice distance
checkInclusion          Check for subset inclusion
clustering              Cluster genesets.
deprecated              Deprecated functions in GeDi
distanceDendro          Plot a dendrogram
distanceHeatmap         Plot a heatmap
enrichmentWordcloud     Visualize the results of an enrichment analysis
                        as word cloud
fuzzyClustering         Find cluster from initial seeds
getAdjacencyMatrix      Construct an adjacency matrix
getAnnotation           Get the annotation of a STRINGdb object
getBipartiteGraph       Construct a bipartite graph
getClusterAdjacencyMatrix
                        Construct an adjacency matrix
getGenes                Split string of genes
getGraphTitle           Build up the node title
getId                   Get NCBI ID
getInteractionScore     Calculate interaction score for two genesets
getJaccardMatrix        Get Matrix of Jaccard distances
getKappaMatrix          Get Matrix of Kappa distances
getMeetMinMatrix        Get Matrix of Meet-Min distances
getPPI                  Download Protein-Protein Interaction (PPI)
getSorensenDiceMatrix   Get Matrix of Sorensen-Dice distances
getStringDB             Get the STRING db entry of a species
getpMMMatrix            Calculate the pMM distance
goDistance              Calculate similarity of GO terms
gsHistogram             Create a histogram plot for gene set sizes
kMeansClustering        Calculate clusters based on kMeans clustering
kNN_clustering          Calculate clusters based on kNN clustering
louvainClustering       Cluster genesets using Louvain clustering.
macrophage_KEGG_example
                        A sample input RData file
macrophage_Reactome_example
                        A sample input RData file
macrophage_topGO_example
                        A sample input RData file
macrophage_topGO_example_small
                        A small sample input RData file
markovClustering        Cluster genesets using Markov clustering.
pMMlocal                Calculate local pMM distance
pamClustering           Calculate clusters based on PAM clustering
ppi_macrophage_topGO_example_small
                        PPI
prepareGenesetData      Split string of genes
sample_geneset          A sample input text file
sample_geneset_broken   A broken input text file
sample_geneset_empty    An empty input text file
sample_geneset_small    A small sample input text file
scaleGO                 Scaling (distance) scores
scores_macrophage_topGO_example_small
                        Sample scores
seedFinding             Find clustering seeds
