BiclustGUI

The BiclustGUI R package, a graphical user interface (GUI) developed as a plug-in for R Commander, is an envelope package designed to serve as a platform from which several biclustering algorithms as well as diagnostics tools can be accessed.

Short Summary

The package RcmdrPlugin.BiclustGUI is a GUI plugin for R Commander (Fox, 2007) for biclustering. It combines different biclustering packages to provide many algorithms, visualisations and diagnostics tools in one unified framework. By choosing R Commander, the BiclustGUI will also create the original R code in the background while using the interface. Since this generated code can be edited and saved, the BiclustGUI is also interesting for more experienced R users who would like to transition from the interface to actual R code after using the algorithms. Further, in order to provide a joint development programming environment ,the BiclustGUI also contains easy template scripts with which future developers can create their own biclustering windows without any knowledge about the tcltk package, which is normally required.

Installation

To be able to the the BiclustGUI, the packages which it depends on should also be installed. Some of them are available on CRAN while others are available on Bioconductor. To install all of the dependencies as well as the BiclustGUI itself, please follow the code below. If any issues with the dependencies arise during the automatic installation, please refer to the manual installation to install the GUI. Note that on the first use of R Commander, you will be prompted to install a couple other dependencies which will be done automatically.

############################################# ## AUTOMATIC INSTALLATION FOR CRAN RELEASE ## #############################################

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

#################################################### ## AUTOMATIC INSTALLATION FOR DEVELOPMENT RELEASE ## ####################################################

## R-Forge ##

setRepositories(ind=c(1:5))

# Biclust GUI - In Development Version # install.packages("RcmdrPlugin.BiclustGUI", repos="http://R-Forge.R-project.org")

# Biclust GUI (ISA2 VERSION) - In Development Version # install.packages("RcmdrPlugin.BiclustGUI.Extra", repos="http://R-Forge.R-project.org")

## GitHub ##

setRepositories(ind=c(1:5)) install.packages("devtools") devtools::install_github("ewouddt/RcmdrPlugin.BiclustGUI")

################################################# ## MANUAL INSTALLATION ## #################################################

## PACKAGES AVAILABLE ON CRAN ## install.packages("biclust") install.packages("BcDiag") install.packages("superbiclust") install.packages("Rcmdr") install.packages("isa2") install.packages("s4vd")
install.packages("BiBitR") install.packages("gplots") install.packages("viridis")

## PACKAGES AVAILABLE ON BIOCONDUCTOR ## source("http://bioconductor.org/biocLite.R") biocLite("iBBiG") biocLite("fabia") biocLite("rqubic") biocLite("BicARE")

## BiclustGUI - CRAN Release Version ## install.packages("RcmdrPlugin.BiclustGUI")

## Biclust GUI - R-Forge - In Development Version ## install.packages("RcmdrPlugin.BiclustGUI", repos="http://R-Forge.R-project.org")

## Biclust GUI (ISA2 VERSION) - R-Forge - In Development Version ## install.packages("RcmdrPlugin.BiclustGUI.Extra", repos="http://R-Forge.R-project.org")

## Biclust GUI - GitHub - In Development Version ## install.packages("devtools") devtools::install_github("ewouddt/RcmdrPlugin.BiclustGUI")

Once all dependencies are installed, to launch the BiclustGUI, open R and use the library(RcmdrPlugin.BiclustGUI) command.

Personal tools

BiclustGUI

Short Summary

Installation