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... |
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... |
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... |
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... |
ContFeaturesPlot | Plot of continuous features |
DetermineWeight_SilClust | Determines an optimal weight for weighted clustering by... |
DetermineWeight._SimClust | Determines an optimal weight for weighted clustering by... |
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... |
FindElement | Find an element in a data structure |
FindGenes | Investigates whether genes are differential expressed in... |
fingerprintMat | The fingerprint matrix for the MCF7 data |
GeneInfo | The gene info data frame |
geneMat | The gene expression matrix |
Geneset.intersect | Intersection over resulting gene sets of 'PathwaysIter'... |
GS | List of GO Annotations |
HeatmapPlot | Comparing two clustering results with a heatmap |
HeatmapSelection | A function to select a group of compounds via the similarity... |
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... |
SelectnrClusters | Determines an optimal number of clusters based on silhouette... |
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... |
SNF | Similarity Network Fusion |
SNFa | Similarity Network Fusion - version a |
SNFb | Similarity Network Fusion - version b |
SNFc | Similarity Network Fusion - version c |
targetMat | The target prediction matrix |
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 |
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