Man pages for rforge/intclust
Integrated Data Analysis via Clustering
| 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 |
