In ewouddt/RcmdrPlugin.BiclustGUI: 'Rcmdr' Plug-in GUI for Biclustering

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)

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 (1.1.3), please use the following commands:

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

To install the Development Version from GitHub repository use:

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

| R Package | Biclustering Method | Publication | |----------|----------------------------|----------------| | biclust | Plaid | Turnet et al., 2005 | | biclust | $\delta$-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 |