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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 (1.1.1), 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")

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 version is <= 1.12 (recursive dependencies bug)

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

Introductory Blog on GitHub/R-Bloggers (See Blogpost).
Detailed Guide (See Vignette).
Shiny Application for Biclustering (Shiny Cloud + Stand-Alone + GitHub (Coming Soon))
R-Forge Project Page (R-Forge).
I-Biostat Page (I-Biostat).

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

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.