README.md

In RcmdrPlugin.BiclustGUI.Extra: Title: 'Rcmdr' Plug-in GUI for Biclustering

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")

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 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

RcmdrPlugin.BiclustGUI.Extra documentation built on May 2, 2019, 5:19 p.m.