IntClust-package | Integrated Clustering Methods. |
ABC.SingleInMultiple | Single-source ABC clustering |
ADC | Aggregated data clustering |
ADEC | Aggregated data ensemble clustering |
BinFeaturesPlot_MultipleData | Visualization of characteristic binary features of multiple data sets |
BinFeaturesPlot_SingleData | Visualization of characteristic binary features of a single data set |
BoxPlotDistance | Box plots of one distance matrix categorized against another distance matrix. |
CEC | Complementary ensemble clustering |
CharacteristicFeatures | Determining the characteristic features of a cluster |
ChooseCluster | Interactive plot to determine DE Genes and DE features for a specific cluster |
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 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. |
ConsensusClustering | Consensus clustering |
ContFeaturesPlot | Plot of continuous features |
CVAA | Cumulative voting-based aggregation algorithm |
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 |
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 |
f.gsample | f.gsample |
f.rmv | f.rmv |
f.t | ff |
FeatSelection | feature selection for a selection of objects |
FeaturesOfCluster | List all features present in a selected cluster of objects |
FindCluster | Find a selection of objects in the output of 'ReorderToReference' |
FindElement | Find an element in a data structure |
FindGenes | Investigates whether genes are differential expressed in multiple clusters |
fingerprintMat | Fingerprint data |
GeneInfo | Information of the genes Gene info in a data frame |
geneMat | Gene expression data |
Geneset.intersect | Intersection over resulting gene sets of 'PathwaysIter' function |
Geneset.intersectSelection | Intersection over resulting gene sets of 'PathwaysIter' function for a selection of objects |
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 heatmap. |
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 reference |
SelectnrClusters | Determines an optimal number of clusters based on silhouette widths |
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 a selection of objects. |
SharedSelectionLimma | Intersection of genes over multiple methods for a selection of objects. |
SharedSelectionMLP | Intersection of pathways over multiple methods for a selection of objects. |
SimilarityHeatmap | A heatmap of similarity values between objects |
SimilarityMeasure | A measure of similarity for the outputs of the different methods |
SNF | Similarity network fusion |
targetMat | Target prediction data |
TrackCluster | Follow a cluster over multiple methods |
WeightedClust | Weighted clustering |
WonM | Weighting on membership |