rqubic: Qualitative biclustering algorithm for expression data analysis in R

This package implements the QUBIC algorithm introduced by Li et al. for the qualitative biclustering with gene expression data.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("rqubic")
AuthorJitao David Zhang, with inputs from Laura Badi and Martin Ebeling
Bioconductor views Clustering Microarray
Date of publicationNone
MaintainerJitao David Zhang <jitao_david.zhang@roche.com>
LicenseGPL-2
Version1.20.0

View on Bioconductor

Functions

BCconditionCount Man page
BCconditionCount,Biclust,ANY-method Man page
BCconditionCount,Biclust,missing-method Man page
BCconditions Man page
BCconditions,Biclust,ANY-method Man page
BCconditions,Biclust,missing-method Man page
BCcount Man page
BCcount,Biclust-method Man page
BCfeatureCount Man page
BCfeatureCount,Biclust,ANY-method Man page
BCfeatureCount,Biclust,missing-method Man page
BCfeatures Man page
BCfeatures,Biclust,ANY-method Man page
BCfeatures,Biclust,missing-method Man page
[,Biclust,ANY,missing,missing-method Man page
combineBiclusts Man page
combineBiclusts,Biclust,Biclust-method Man page
combineBiclusts,list,missing-method Man page
combineBiclusts-methods Man page
combineBiclusts,QUBICBiclusterSet,QUBICBiclusterSet-method Man page
conditionCount Man page
conditionCount,Biclust-method Man page
conditionCount-methods Man page
conditionCount,QUBICBicluster-method Man page
conditions Man page
conditions,Biclust-method Man page
conditions-methods Man page
eSetDimName Man page
fcFilter Man page
fcFilter,Biclust-method Man page
fcFilter-methods Man page
featureCount Man page
featureCount,Biclust-method Man page
featureCount-methods Man page
featureCount,QUBICBicluster-method Man page
featureNames,Biclust-method Man page
features Man page
features,Biclust-method Man page
features-methods Man page
generateSeeds Man page
generateSeeds,eSet-method Man page
generateSeeds,matrix-method Man page
generateSeeds-methods Man page
info Man page
info,Biclust,ANY-method Man page
info,Biclust,missing-method Man page
NumberxCol Man page
NumberxCol,Biclust-method Man page
parameter Man page
parameter,Biclust,character-method Man page
parameter,Biclust,missing-method Man page
parseQubicBlocks Man page
parseQubicChars Man page
parseQubicRules Man page
quantileDiscretize Man page
quantileDiscretize,eSet-method Man page
quantileDiscretize,matrix-method Man page
quantileDiscretize-methods Man page
QUBICBiclusterSet-class Man page
quBicluster Man page
readBiclusterResults Man page
RowxNumber Man page
RowxNumber,Biclust-method Man page
rqubic Man page
rqubic-package Man page
sampleNames,Biclust-method Man page
show,QUBICBiclusterSet-method Man page
Svalue Man page
Svalue,eSet,missing-method Man page
Svalue,matrix,missing-method Man page
Svalue,QUBICBiclusterSet,ANY-method Man page
Svalue,QUBICBiclusterSet,missing-method Man page
writeQubicInputFile Man page

Files

DESCRIPTION
Makefile
NAMESPACE
NEWS
R
R/AllClasses.R R/AllMethods.R R/c_output_parser.R R/combineBiclust.R R/onload.R R/r_qubic_implementation.R R/readBiclusterResults.R R/rqubic_to_c_funcs.R
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/rqubic.R
inst/doc/rqubic.Rnw
inst/doc/rqubic.pdf
inst/extdata
inst/extdata/bic_1.out
inst/extdata/bic_3.out
inst/extdata/bic_null.out
inst/extdata/sampleExpressionSet.blocks
inst/extdata/sampleExpressionSet.chars
inst/extdata/sampleExpressionSet.rules
man
man/QUBICBiclusterSet-class.Rd man/combineBiclusts-methods.Rd man/discretize.Rd man/eSetDimName.Rd man/fcFilter-methods.Rd man/fcFilter.Rd man/features-methods.Rd man/generateSeeds-methods.Rd man/parseQubicBlocks.Rd man/quBicluster.Rd man/readBiclusterResults.Rd man/rqubic-package.Rd man/writeQubicInputFile.Rd
src
src/bicluster.c
src/bicluster.h
src/discretize.c
src/fib.c
src/fib.h
src/graph.c
src/graph.h
src/rqubic.c
src/rqubic.h
tests
tests/c_output_parser_tests.R tests/rqubic_implementations.R tests/test_read.R tests/test_utilities.R
vignettes
vignettes/backup.sty
vignettes/rqubic.Rnw
vignettes/rqubic.bib

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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