ADC                     Aggregated Data Clustering
ADEC                    Aggregated Data Ensemble Clustering
ADECa                   Aggregated Data Ensemble Clustering - version a
ADECb                   Aggregated Data Ensemble Clustering - version b
ADECc                   Aggregated Data Ensemble Clustering - version c
BinFeaturesPlot         Plot of a selection of features
BoxPlotDistance         Box plots of one distance matrix categorized
                        against another distance matrix.
CEC                     Complementary Ensemble Clustering
CECa                    Complementary Ensemble Clustering - version a
CECb                    Complementary Ensemble Clustering - version b
CECc                    Complementary Ensemble Clustering - version c
CharacteristicFeatures
                        Determining the characteristic features of a
                        cluster
ChooseCluster           Interactive plot to determine DE Genes and DE
                        features for a specific cluster
Cluster                 Perform clustering on a single data source
ClusterPlot             Plot a dendrogram with leaves colored by a
                        result of choice
ColorPalette            Create a color palette to be used in the plots
Colors1                 First example for colors
Colors2                 Second example for colors
ColorsNames             Function that annotates colors to their names
CompareInteractive      Interactive comparison of clustering results
                        for a specific cluster or method.
ComparePlot             Comparison of clustering results over multiple
                        results
CompareSilCluster       Compares medoid clustering results based on
                        silhouette widths
CompareSvsM             Comparison of clustering results for the single
                        and multiple source clustering.
ContFeaturesPlot        Plot of continuous features
DetermineWeight_SilClust
                        Determines an optimal weight for weighted
                        clustering by silhouettes widths.
DetermineWeight_SimClust
                        Determines an optimal weight for weighted
                        clustering by similarity weighted clustering.
DiffGenes               Differential gene expressions for multiple
                        results
Distance                Distance function
FeaturesOfCluster       Lists all features present in a selected
                        cluster of compounds
FindCluster             Find a selection of compounds in the output of
                        'ReorderToReference'
FindElement             Find an element in a data structure
FindGenes               Investigates whether genes are differential
                        expressed in multiple clusters
GS                      List of GO Annotations
GeneInfo                The gene info data frame
Geneset.intersect       Intersection over resulting gene sets of
                        'PathwaysIter' function
HeatmapPlot             Comparing two clustering results with a heatmap
HeatmapSelection        A function to select a group of compounds via
                        the similarity heatmap.
IntClust-package        Integrated Data Analysis
LabelPlot               Coloring specific leaves of a dendrogram
Normalization           A normalization function
PathwayAnalysis         Pathway Analysis
Pathways                Pathway analysis for multiple clustering
                        results
PathwaysIter            Iterations of the pathway analysis
PlotPathways            A GO plot of a pathway analysis output.
PreparePathway          Preparing a data set for pathway analysis
ProfilePlot             Plotting gene profiles
ReorderToReference      Order the outputs of the clustering methods
                        against a reference
SNF                     Similarity Network Fusion
SNFa                    Similarity Network Fusion - version a
SNFb                    Similarity Network Fusion - version b
SNFc                    Similarity Network Fusion - version c
SelectnrClusters        Determines an optimal number of clusters based
                        on silhouette widths
SharedComps             Intersection of clusters over multiple methods
SharedGenesPathsFeat    Intersection of genes and pathways over
                        multiple methods
SimilarityHeatmap       A heatmap of similarity values between
                        compounds
SimilarityMeasure       A measure of similarity for the outputs of the
                        different methods
TrackCluster            Follow a cluster over multiple methods
Ultimate                Function that performs any aggregated data
                        function
WeightedClust           Weighted clustering
WeightedSimClust        Weighted similarity clustering
WonM                    Weighting on Membership
fingerprintMat          The fingerprint matrix for the MCF7 data
geneMat                 The gene expression matrix
targetMat               The target prediction matrix
