biclust: BiCluster Algorithms
Version 1.2.1

The main function biclust provides several algorithms to find biclusters in two-dimensional data: Cheng and Church, Spectral, Plaid Model, Xmotifs and Bimax. In addition, the package provides methods for data preprocessing (normalization and discretisation), visualisation, and validation of bicluster solutions.

Browse man pages Browse package API and functions Browse package files

AuthorSebastian Kaiser, Rodrigo Santamaria, Tatsiana Khamiakova, Martin Sill, Roberto Theron, Luis Quintales, Friedrich Leisch and Ewoud De Troyer.
Date of publication2015-12-11 12:45:49
MaintainerSebastian Kaiser <Sebastian.Kaiser@stat.uni-muenchen.de>, Ewoud De Troyer <ewoud.detroyer@uhasselt.be>
LicenseGPL-3
Version1.2.1
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("biclust", repos="http://R-Forge.R-project.org")

Man pages

BCBimax: The Bimax Bicluster algorithm
BCCC: The CC Bicluster algorithm
BCPlaid: The Plaid Model Bicluster algorithm
BCQuest: The Questmotif Bicluster algorithm
BCSpectral: The Spectral Bicluster algorithm
BCXmotifs: The Xmotifs Bicluster algorithm
BicatYeast: BicAT Yeast
Biclust: The Biclust Class
biclustbarchart: Bicluster Barchart
bicluster: Extract Bilcuster
biclust-method: The biclust Method
BiclustMethod: The BiclustMethod Virtual Class
bimax.grid: Parameter Grid for BCBimax Biclustering
binarize: Binarize
bubbleplot: Bubbleplot
ChiaKaruturi: Chia and Karuturi Function
clustmember: Bicluster Membership Graph
coherence: Coherence measures
computeObservedFstat: Diagnostic F Statistic Calculation
diagnoseColRow: Bootstrap Procedure for Bicluster Diagnostics
diagnosticPlot: Diagnostic F Statistics Visualization
discretize: Create a discret matrix
drawHeatmap: Draw Heatmap
EisenYeast: Eisen Yeast
ensemble: Ensemble Methods for Bicluster Algorithms
heatmapBC: Overlapping Heatmap
isoverlapp: Is Bicresult overlapping?
jaccard: Jaccardind
parallelCoordinates: Parallel Coordinates
plaid.grid: Parameter Grid for BCPlaid Biclustering
plotclust: Barplot of Bicluster
predict: Predict from a BCrepBimax Result
SyntrenEcoli: SynTReN E. coli
writeBiclusterResults: writeBiclusterResults
writeclust: Write a Bicluster as a Cluster Result

Functions

BCBimax Man page Source code
BCBimax-class Man page
BCCC Man page Source code
BCCC-class Man page
BCPlaid Man page Man page Source code
BCPlaid-class Man page
BCQuest Man page Source code
BCQuest-class Man page
BCQuestmet Man page Source code
BCQuestmet-class Man page
BCQuestord Man page Source code
BCQuestord-class Man page
BCSpectral Man page Source code
BCSpectral-class Man page
BCXmotifs Man page Source code
BCXmotifs-class Man page
BCrepBimax Man page Source code
BCrepBimax-class Man page
Barchart Source code
BicatYeast Man page
Biclust Man page
Biclust-class Man page
BiclustMethod Man page
BiclustMethod-class Man page
BiclustResult Man page Source code
Bimax Man page
CC Man page
ChiaKaruturi Man page Source code
E. coli microarray synthetic data matrix Man page
EisenYeast Man page
Escherichia Coly data matrix generated by SynTReN Man page
Kluger biclustering Man page
Quest Man page
Saccharomices Cerevisiae data matrix Man page
Saccharomices Cerevisiae reduced data matrix Man page
SyntrenEcoli Man page
Xmotif Man page
addcolscore Source code
additiveVariance Man page Source code
addrowscore Source code
backFit Source code
biclust Man page
biclust,matrix,BCBimax-method Man page
biclust,matrix,BCCC-method Man page
biclust,matrix,BCPlaid-method Man page
biclust,matrix,BCQuest-method Man page
biclust,matrix,BCQuestmet-method Man page
biclust,matrix,BCQuestord-method Man page
biclust,matrix,BCSpectral-method Man page
biclust,matrix,BCXmotifs-method Man page
biclust,matrix,BCrepBimax-method Man page
biclust,matrix,BiclustMethod-method Man page
biclust,matrix,character-method Man page
biclust,matrix,function-method Man page
biclust-method Man page
biclustbarchart Man page Source code
bicluster Man page Source code
biclusterES Source code
biclusternumber Man page Source code
biclustmember Man page Source code
bicorder Man page Source code
bigcc Source code
biggest Source code
bigquestmetmotif Source code
bigquestmotif Source code
bigquestordmotif Source code
bigxmotif Source code
bimax.grid Man page Source code
bimaxbiclust Source code
binarize Man page Source code
binarizeByPercentage Man page Source code
bistochastization Source code
bubble plot Man page
bubbleplot Man page Source code
cbimax Source code
cc.grid Source code
cc1 Source code
cc2 Source code
cc3 Source code
ccbiclust Source code
ccscore Source code
clustmember Man page Source code
coherence Man page
coherenceAnalysis Source code
colscore Source code
computeObservedFstat Man page Source code
constantVariance Man page Source code
convertclust Source code
corappr Source code
createBarchartPanel Source code
densityOnes Man page Source code
diagnoseColRow Man page Source code
diagnosticPlot Man page Source code
dif Source code
discretize Man page Source code
distributeList Source code
div Source code
drawHeatmap Man page Source code
drawHeatmap2 Man page Source code
ensemble Man page Source code
filterclust Source code
firstcome Source code
fitLayer Source code
hcl Source code
heatmap Man page
heatmapBC Man page Source code
heatorder Source code
iaddrowscore Source code
irrc Source code
isoverlapp Man page Source code
iterativeKmeans Source code
jaccard1 Source code
jaccard2 Man page Source code
jaccardind Man page Source code
kmeansClassStart Source code
kmeansStart Source code
logical2sparse Source code Source code Source code
logt Source code
makeLayer Source code
maxbimaxbiclust Source code
multiplicativeVariance Man page Source code
normalization Source code
overallVariance Source code
overlap Source code
parallel coordinates Man page
parallelCoordinates Man page Source code
plaid Man page Source code
plaid model Man page
plaid.grid Man page Source code
plotclust Man page Man page Source code
postprocess Source code
predictBimax Man page Source code
prequest Source code
printrect Source code
qtbiggest Source code
questmetmotif Source code
questmotif Source code
questordmotif Source code
repBimax Man page
repbimaxbiclust Source code
rodrigo2sebastian Source code
rowscore Source code
sebastian2rodrigo Source code
show,Biclust-method Man page
sig Source code
signVariance Man page Source code
spectral Man page Source code
spectral biclustering Man page
spectral.grid Source code
star graph Man page
storexmotif Source code
summary,Biclust-method Man page
turner biclustering Man page
updatePlaid Source code
variance Source code
withinVar Source code Source code
writeBiclusterResults Man page Source code
writeBiclusters Man page
writeclust Man page Source code
xmotif.grid Source code
xmotifbiclust Source code
yeast microarray data matrix Man page
yeast microarray reduced data matrix Man page

Files

COPYING
DESCRIPTION
NAMESPACE
NEWS
R
R/DiagnosticsFunctions.R
R/aaa-biclust.r
R/biclustbarchart.r
R/bicluster.r
R/bicorder.r
R/bimax.r
R/binarize.r
R/bubbleplot.r
R/cc.r
R/clustmember.r
R/coherence.r
R/drawHeatmap.r
R/drawHeatmap2.r
R/ensemble.R
R/heatmap.r
R/helpers.r
R/isoverlapp.r
R/iterativekmeans.r
R/jaccard.r
R/logical2sparse.r
R/normalization.r
R/parallelCoordinates.r
R/plaid.r
R/postprocessing.r
R/predict.r
R/questmetmotif.r
R/questmotif.r
R/questordmotif.r
R/spectral.r
R/writeBiclusterResults.r
R/xmotif.r
data
data/BicatYeast.rda
data/EisenYeast.rda
data/SyntrenEcoli.rda
data/datalist
man
man/BCBimax.rd
man/BCCC.rd
man/BCPlaid.Rd
man/BCQuest.rd
man/BCSpectral.Rd
man/BCXmotifs.rd
man/BicatYeast.Rd
man/Biclust.rd
man/BiclustMethod.rd
man/ChiaKaruturi.Rd
man/EisenYeast.Rd
man/SyntrenEcoli.Rd
man/biclust-method.rd
man/biclustbarchart.rd
man/bicluster.rd
man/bimax.grid.Rd
man/binarize.Rd
man/bubbleplot.Rd
man/clustmember.rd
man/coherence.Rd
man/computeObservedFstat.Rd
man/diagnoseColRow.Rd
man/diagnosticPlot.Rd
man/discretize.rd
man/drawHeatmap.Rd
man/ensemble.Rd
man/heatmapBC.Rd
man/isoverlapp.rd
man/jaccard.rd
man/parallelCoordinates.Rd
man/plaid.grid.Rd
man/plotclust.rd
man/predict.rd
man/writeBiclusterResults.Rd
man/writeclust.rd
src
src/rbimax.c
biclust documentation built on May 21, 2017, 3:31 a.m.