IntClust: Integrated Data Analysis via Clustering

Several integrative data methods in which information of objects from different data sources can be combined are included in the IntClust package. As a single data source is limited in its point of view, this provides more insight and the opportunity to investigate how the variables are interconnected. Clustering techniques are to be applied to the combined information. For now, only agglomerative hierarchical clustering is implemented. Further, differential gene expression and pathway analysis can be conducted on the clusters. Plotting functions are available to visualize and compare results of the different methods.

AuthorMarijke Van Moerbeke
Date of publication2016-02-15 07:51:46
MaintainerMarijke Van Moerbeke <marijkevanmoerbeke@uhasselt.be>
LicenseGPL-3
Version0.0.1

View on R-Forge

Man pages

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

Files in this package

IntClust/DESCRIPTION
IntClust/NAMESPACE
IntClust/R
IntClust/R/ADC.R IntClust/R/ADEC.R IntClust/R/ADECa.R IntClust/R/ADECb.R IntClust/R/ADECc.R IntClust/R/BinFeaturesPlot.R IntClust/R/BoxPlotDistance.R IntClust/R/CEC.R IntClust/R/CECa.R IntClust/R/CECb.R IntClust/R/CECc.R IntClust/R/CharacteristicsFeatures.R IntClust/R/ChooseCluster.R IntClust/R/Cluster.R IntClust/R/ClusterCols.R IntClust/R/Clusterplot.R IntClust/R/Colorpalette.R IntClust/R/ColorsNames.R IntClust/R/CompareInteractive.R IntClust/R/ComparePlot.R IntClust/R/CompareSilCluster.R IntClust/R/CompareSvsM.R IntClust/R/ContFeaturesPlot.R IntClust/R/DetermineWeight_SilClust.R IntClust/R/DetermineWeight_SimClust.R IntClust/R/DiffGenes.R IntClust/R/DiffGenesSelection.R IntClust/R/Distance.R IntClust/R/FeatSelection.R IntClust/R/FeaturesOfCluster.R IntClust/R/FindCluster.R IntClust/R/FindElement.R IntClust/R/FindGenes.R IntClust/R/Geneset.intersect.R IntClust/R/Geneset.intersectSelection.R IntClust/R/HeatmapPlot.R IntClust/R/HeatmapSelection.R IntClust/R/IntClust-internal.R IntClust/R/LabelCols.R IntClust/R/Labelplot.R IntClust/R/Normalization.R IntClust/R/PathwayAnalysis.R IntClust/R/Pathways.R IntClust/R/PathwaysIter.R IntClust/R/PathwaysSelection.R IntClust/R/PlotPathways.R IntClust/R/PreparePathway.R IntClust/R/ProfilePlot.R IntClust/R/ReorderToReference.R IntClust/R/SNF.R IntClust/R/SNFa.R IntClust/R/SNFb.R IntClust/R/SNFc.R IntClust/R/SelectnrClusters.R IntClust/R/SharedComps.R IntClust/R/SharedGenesPathsFeat.R IntClust/R/SharedSelection.R IntClust/R/SharedSelectionLimma.R IntClust/R/SharedSelectionMLP.R IntClust/R/SimilarityHeatmap.R IntClust/R/SimilarityMeasure.R IntClust/R/TrackCluster.R IntClust/R/Ultimate.R IntClust/R/WeightedClust.R IntClust/R/WeightedSimClust.R IntClust/R/WonM.R IntClust/R/distanceheatmaps.R
IntClust/build
IntClust/build/vignette.rds
IntClust/data
IntClust/data/Colors1.RData
IntClust/data/Colors2.RData
IntClust/data/GS.RData
IntClust/data/GeneInfo.rda
IntClust/data/datalist
IntClust/data/fingerprintMat.rda
IntClust/data/geneMat.rda
IntClust/data/targetMat.rda
IntClust/inst
IntClust/inst/doc
IntClust/inst/doc/IntClustVignette.R
IntClust/inst/doc/IntClustVignette.Rnw
IntClust/inst/doc/IntClustVignette.pdf
IntClust/man
IntClust/man/ADC.Rd IntClust/man/ADEC.Rd IntClust/man/ADECa.Rd IntClust/man/ADECb.Rd IntClust/man/ADECc.Rd IntClust/man/BinFeaturesPlot.Rd IntClust/man/BoxPlotDistance.Rd IntClust/man/CEC.Rd IntClust/man/CECa.Rd IntClust/man/CECb.Rd IntClust/man/CECc.Rd IntClust/man/CharacteristicFeatures.Rd IntClust/man/ChooseCluster.Rd IntClust/man/Cluster.Rd IntClust/man/ClusterPlot.Rd IntClust/man/Colorpalette.Rd IntClust/man/Colors1.Rd IntClust/man/Colors2.Rd IntClust/man/ColorsNames.Rd IntClust/man/CompareInteractive.Rd IntClust/man/ComparePlot.Rd IntClust/man/CompareSilCluster.Rd IntClust/man/CompareSvsM.Rd IntClust/man/ContFeaturesPlot.Rd IntClust/man/DetermineWeight._SimClust.Rd IntClust/man/DetermineWeight_SilClust.Rd IntClust/man/DiffGenes.Rd IntClust/man/Distance.Rd IntClust/man/FeaturesOfCluster.Rd IntClust/man/FindCluster.Rd IntClust/man/FindElement.Rd IntClust/man/FindGenes.Rd IntClust/man/GS.Rd IntClust/man/GeneInfo.Rd IntClust/man/Geneset.intersect.Rd IntClust/man/HeatmapPlot.Rd IntClust/man/HeatmapSelection.Rd IntClust/man/IntClust-package.Rd IntClust/man/LabelPlot.Rd IntClust/man/Normalization.Rd IntClust/man/PathwayAnalysis.Rd IntClust/man/Pathways.Rd IntClust/man/PathwaysIter.Rd IntClust/man/PlotPathways.Rd IntClust/man/PreparePathway.Rd IntClust/man/ProfilePlot.Rd IntClust/man/ReorderToReference.Rd IntClust/man/SNF.Rd IntClust/man/SNFa.Rd IntClust/man/SNFb.Rd IntClust/man/SNFc.Rd IntClust/man/SelectnrClusters.Rd IntClust/man/SharedComps.Rd IntClust/man/SharedGenesPathsFeat.Rd IntClust/man/SimilarityHeatmap.Rd IntClust/man/SimilarityMeasure.Rd IntClust/man/TrackCluster.Rd IntClust/man/Ultimate.Rd IntClust/man/WeightedClust.Rd IntClust/man/WeightedSimClust.Rd IntClust/man/WonM.Rd IntClust/man/fingerprintMat.Rd IntClust/man/geneMat.Rd IntClust/man/targetMat.Rd
IntClust/vignettes
IntClust/vignettes/BVSPermbib.bib
IntClust/vignettes/CompareSvsM.pdf
IntClust/vignettes/HeatmapSelection_MCF7W.pdf
IntClust/vignettes/IntClustVignette-ComparePlot.pdf
IntClust/vignettes/IntClustVignette-CompareSvsM.pdf
IntClust/vignettes/IntClustVignette-FeaturesPlotF.pdf
IntClust/vignettes/IntClustVignette-FeaturesPlotFP.pdf
IntClust/vignettes/IntClustVignette-FeaturesPlotT.pdf
IntClust/vignettes/IntClustVignette.Rnw
IntClust/vignettes/Interactive.png
IntClust/vignettes/Interactive1.pdf
IntClust/vignettes/InteractiveCluster.pdf
IntClust/vignettes/InteractiveMethod.pdf
IntClust/vignettes/SimilarityHeatmap_MCF7W.pdf
IntClust/vignettes/Tracking.pdf
IntClust/vignettes/asa.bst

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