'Rcmdr' Plug-in GUI for Biclustering

A plug-in for R Commander ('Rcmdr'). The package is a Graphical User Interface (GUI) in which several biclustering methods can be executed, followed by diagnostics and plots of the results. Further, the GUI also has the possibility to connect the methods to more general diagnostic packages for biclustering. Biclustering methods from 'biclust', 'fabia', 's4vd', 'iBBiG', 'isa2', 'BiBitR', 'rqubic' and 'BicARE' are implemented. Additionally, 'superbiclust' and 'BcDiag' are also implemented to be able to further investigate results. The GUI also provides a couple of extra utilities to export, save, search through and plot the results. 'RcmdrPlugin.BiclustGUI' also provides a very specific framework for biclustering in which new methods, diagnostics and plots can be added. Scripts were prepared so that R-package developers can freely design their own dialogs in the GUI which can then be added by the maintainer of 'RcmdrPlugin.BiclustGUI'. These scripts do not required any knowledge of 'tcltk' and 'Rcmdr' and are easy to fill in.


The BiclustGUI for R Commander

RcmdrPlugin.BiclustGUI is a R Commander Plug-In containing multiple methods to apply biclustering and visualise these results.

Installing the GUI

To install the CRAN Release Version (1.1.0), please use the following commands:

setRepositories(ind=c(1:5))
install.packages("RcmdrPlugin.BiclustGUI")

To install the Development Version from either the R-Forge or GitHub repository use:

setRepositories(ind=c(1:5))
install.packages("RcmdrPlugin.BiclustGUI",repos="http://R-Forge.R-project.org")

or

setRepositories(ind=c(1:5))
install.packages("devtools") # If not yet installed on your R Version
devtools::install_github("hadley/devtools") # Only run this if your currently installed 
 
devtools::install_github("ewouddt/RcmdrPlugin.BiclustGUI")

One of the options above will install the GUI and its dependencies from both CRAN and Bioconductor. Should some issue arise with a package installation, please try to manual install them. The code for this can be found here.

On the initial start-up of R Commander, you will probably be prompted to install some additional dependencies. This should not take too long!

To launch the GUI, use:

library(RcmdrPlugin.BiclustGUI)

More Info & Links

Currently Available Methods/Diagnostics

All included biclustering and diagnostics packages in the BiclustGUI:
R Package Biclustering Method Publication
biclust Plaid Turnet et al., 2005
biclust δ-biclustering Cheng and Church, 2000
biclust X Motif Murali and Kasif, 2003
biclust Spectral Kluger et al., 2003
biclust QuestMotif Kaiser, 2011
biclust Bimax Prelic et al., 2006
fabia FABIA Hochreiter et al., 2010
isa2 The Iterative Signature Algorithm Bergman et al., 2003
iBBiG Iterative Binary Biclustering of Genesets Gusenleitner et al., 2012
rqubic Qualitative Biclustering Li et al., 2009
BicARE Biclustering Analysis and Results Exploration Gestraud and Barillot, 2014
s4vd SSVD (Sparse Singular Value Decomposition) Lee et al., 2010
s4vd S4VD (SSVD incorporating stability correction) Sill et al., 2011
BiBitR Biclustering Algorithm for extracting bit-patterns from binary data-sets Rodriguez-Baena et al., 2011
R Package Diagnostics Publication
BcDiag Bicluster Diagnostic Plots Aregay et al., 2014
superbiclust Generating Robust Biclusters from a Bicluster Set Khamiakova, 2013

News

  • First version release (2016)

Reference manual

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install.packages("RcmdrPlugin.BiclustGUI")

1.1.1 by De Troyer Ewoud, 2 years ago


Browse source code at https://github.com/cran/RcmdrPlugin.BiclustGUI


Authors: De Troyer Ewoud , Otava Martin


Documentation:   PDF Manual  


GPL-3 license


Imports Rcmdr, tcltk, gplots, grDevices, graphics, methods, utils, viridis

Depends on biclust, fabia, iBBiG, superbiclust, BcDiag, rqubic, BicARE, s4vd, BiBitR

Suggests knitr


See at CRAN