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. (Note: rqubic currently requires manual installation through BiocManager::install('rqubic').)
RcmdrPlugin.BiclustGUI is a R Commander Plug-In containing multiple methods to apply biclustering and visualise these results.
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 Versiondevtools::install_github("hadley/devtools") # Only run this if your currently installeddevtools::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)
| 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 |