Man pages for IntClust
Integration of Multiple Data Sets with Clustering Techniques
| ABC.SingleInMultiple | Single-source ABC clustering |
| ADC | Aggregated data clustering |
| ADEC | Aggregated data ensemble clustering |
| BinFeaturesPlot_MultipleData | Visualization of characteristic binary features of multiple... |
| BinFeaturesPlot_SingleData | Visualization of characteristic binary features of a single... |
| BoxPlotDistance | Box plots of one distance matrix categorized against another... |
| CEC | Complementary ensemble clustering |
| CharacteristicFeatures | Determining the characteristic features of a cluster |
| ChooseCluster | Interactive plot to determine DE Genes and DE features for a... |
| Cluster | Single source clustering |
| ClusterCols | Matching clusters with colours |
| ClusteringAggregation | Clustering aggregation |
| ClusterPlot | Colouring clusters in a dendrogram |
| ColorPalette | Create a color palette to be used in the plots |
| Colors1 | Colour examples |
| 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... |
| ConsensusClustering | Consensus clustering |
| ContFeaturesPlot | Plot of continuous features |
| CVAA | Cumulative voting-based aggregation algorithm |
| 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 |
| DiffGenesSelection | Differential expression for a selection of objects |
| Distance | Distance calculation |
| distanceheatmaps | Determine the distance in a heatmap |
| EHC | Ensemble for hierarchical clustering |
| EnsembleClustering | Ensemble clustering |
| EvidenceAccumulation | Evidence accumulation |
| f.clustABC.MultiSource | f.clustABC.MultiSoucre |
| FeatSelection | feature selection for a selection of objects |
| FeaturesOfCluster | List all features present in a selected cluster of objects |
| f.gsample | f.gsample |
| FindCluster | Find a selection of objects in the output of... |
| FindElement | Find an element in a data structure |
| FindGenes | Investigates whether genes are differential expressed in... |
| fingerprintMat | Fingerprint data |
| f.rmv | f.rmv |
| f.t | ff |
| GeneInfo | Information of the genes Gene info in a data frame |
| geneMat | Gene expression data |
| Geneset.intersect | Intersection over resulting gene sets of 'PathwaysIter'... |
| Geneset.intersectSelection | Intersection over resulting gene sets of 'PathwaysIter'... |
| GS | List of GO Annotations |
| HBGF | Hybrid bipartite graph formulation |
| HeatmapPlot | Comparing two clustering results with a heatmap |
| HeatmapSelection | A function to select a group of objects via the similarity... |
| HierarchicalEnsembleClustering | Hierarchical ensemble clustering |
| IntClust | Integrated Clustering Methods. |
| LabelCols | Colouring labels |
| LabelPlot | Coloring specific leaves of a dendrogram |
| LinkBasedClustering | Link based clustering |
| M_ABC | Multi-source ABC clustering |
| Normalization | Normalization of features |
| PathwayAnalysis | Pathway Analysis |
| Pathways | Pathway analysis for multiple clustering results |
| PathwaysIter | Iterations of the pathway analysis |
| PathwaysSelection | Pathway analysis for a selection of objects |
| 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 across multiple methods |
| SharedGenesPathsFeat | Intersection of genes and pathways over multiple methods |
| SharedSelection | Intersection of genes and pathways over multiple methods for... |
| SharedSelectionLimma | Intersection of genes over multiple methods for a selection... |
| SharedSelectionMLP | Intersection of pathways over multiple methods for a... |
| SimilarityHeatmap | A heatmap of similarity values between objects |
| SimilarityMeasure | A measure of similarity for the outputs of the different... |
| SNF | Similarity network fusion |
| targetMat | Target prediction data |
| TrackCluster | Follow a cluster over multiple methods |
| WeightedClust | Weighted clustering |
| WonM | Weighting on membership |
