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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
::install_github("hadley/devtools") # Only run this if your currently installed
devtools# devtools version is <= 1.12 (recursive dependencies bug)
::install_github("ewouddt/RcmdrPlugin.BiclustGUI") devtools
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)
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.
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