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) , plaid model (2005) , xmotifs (2003) and bimax (2006) . In addition, the package provides methods for data preprocessing (normalization and discretisation), visualisation, and validation of bicluster solutions.


Biclust R package

Installation

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

News

First version released on CRAN: 0.5 (2007-11-29): First Release Second version released on CRAN: 0.7.1 (2009-03-13): New Functions added Third version released on CRAN: 0.7.2 (2009-04-24): Small bugs fixed Fourth version released on CRAN: 0.8.1 (2009-05-07): Major bug fixed in code and in algorithm From Version 0.8.2 new part in BICLUSTRESULT-Class, called info containing additional output from algorithms. Also new BCQuest and BCBimax Algorithms are included. Fifth version released on CRAN: 0.9.1 (2009-12-04): First predict method called predictBimax

Version 0.9.3 has a new developed ensemble method including all needed functions

Version 0.9.4 welcomes Tatsiana as a new developer and has now her diagnostic functions included

Version 1.9.0

  • Fix several small bugs including Plaid, Bimax, Tukey Interaction test,...
  • Fix NOTES/ERRORS for new CRAN release (namespace, examples,...)
  • Addition two new functions for interaction testing of biclusters (additive and multiplicative effects)
    • diagnosticTest: New interaction tests and sampling schemes for significance
    • diagnosticPlot2: Uses output of diagnosticTest for distribution plots
  • New author added: Ewoud De Troyer

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("biclust")

2.0.1 by ORPHANED, a year ago


Browse source code at https://github.com/cran/biclust


Authors: Sebastian Kaiser , Rodrigo Santamaria , Tatsiana Khamiakova , Martin Sill , Roberto Theron , Luis Quintales , Friedrich Leisch and Ewoud De Troyer.


Documentation:   PDF Manual  


Task views: Cluster Analysis & Finite Mixture Models, Graphic Displays & Dynamic Graphics & Graphic Devices & Visualization


GPL-3 license


Imports methods, flexclust, additivityTests, tidyr, ggplot2

Depends on MASS, grid, colorspace, lattice

Suggests isa2


Imported by Anthropometry, BiBitR, sigQC.

Depended on by RcmdrPlugin.BiclustGUI, s4vd, superbiclust.

Suggested by BcDiag, isa2, rattle, seriation.


See at CRAN