RcmdrPlugin.BiclustGUI
is a R Commander Plug-In containing multiple methods to apply biclustering and visualise these results.
To install the CRAN Release Version (1.1.1), 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)
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
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