biclust v2.0.1

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BiCluster Algorithms

The main function biclust() provides several algorithms to find biclusters in two-dimensional data: Cheng and Church (2000, ISBN:1-57735-115-0), spectral (2003) <doi:10.1101/gr.648603>, plaid model (2005) <doi:10.1016/j.csda.2004.02.003>, xmotifs (2003) <doi:10.1142/9789812776303_0008> and bimax (2006) <doi:10.1093/bioinformatics/btl060>. In addition, the package provides methods for data preprocessing (normalization and discretisation), visualisation, and validation of bicluster solutions.

Readme

Biclust R package

Installation

Release (1.2.0)

install.packages("biclust")

Development (2.0.0)

install.packages("devtools") # If not yet installed on your R Version
devtools::install_github("Biclustering/biclust")

Description

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.

Example

data(BicatYeast)
res<-biclust(BicatYeast, method=BCPlaid(), verbose=FALSE)
res

Functions in biclust

Name Description
biclustbarchart Bicluster Barchart
computeObservedFstat Diagnostic F Statistic Calculation
bimax.grid Parameter Grid for BCBimax Biclustering
diagnosticPlot Diagnostic F Statistics Visualization
diagnosticPlot2 Diagnostics F Statistiics Visualization
plotclust Barplot of Bicluster
diagnoseColRow Bootstrap Procedure for Bicluster Diagnostics
bubbleplot Bubbleplot
predictBimax Predict from a BCrepBimax Result
coherence Coherence measures
heatmapBC Overlapping Heatmap
isoverlapp Is Bicresult overlapping?
writeBiclusterResults writeBiclusterResults
ensemble Ensemble Methods for Bicluster Algorithms
parallelCoordinates Parallel Coordinates
writeclust Write a Bicluster as a Cluster Result
plaid.grid Parameter Grid for BCPlaid Biclustering
drawHeatmap Draw Heatmap
Biclust-class The Biclust Class
BCCC The CC Bicluster algorithm
BCQuest The Questmotif Bicluster algorithm
BCXmotifs The Xmotifs Bicluster algorithm
binarize Binarize
SyntrenEcoli SynTReN E. coli
EisenYeast Eisen Yeast
ChiaKaruturi Chia and Karuturi Function
BCPlaid The Plaid Model Bicluster algorithm
BCSpectral The Spectral Bicluster algorithm
BCBimax The Bimax Bicluster algorithm
BicatYeast BicAT Yeast
BiclustMethod-class The BiclustMethod Virtual Class
bicluster Extract Bilcuster
biclust The biclust Method
biclustmember Bicluster Membership Graph
diagnosticTest Testing Procedure for Bicluster Diagnostics
discretize Create a discret matrix
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Details

Date 2018-06-09
License GPL-3
LazyLoad yes
Repository CRAN
RoxygenNote 6.0.1
NeedsCompilation yes
Packaged 2018-06-09 13:54:25 UTC; ripley
X-CRAN-Original-Maintainer Sebastian Kaiser
X-CRAN-Comment Orphaned and corrected on 2018-06-09 as check errors were ignored despite reminders. Use of uninitialized memory, major leaks detected by valgrind. fflush(stdin) is undefined behaviour (or pointless in POSIX 2008).
Date/Publication 2018-06-09 16:25:13 UTC

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