rqubic: Qualitative biclustering algorithm for expression data analysis in R

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

Author
Jitao David Zhang, with inputs from Laura Badi and Martin Ebeling
Date of publication
None
Maintainer
Jitao David Zhang <jitao_david.zhang@roche.com>
License
GPL-2
Version
1.20.0

View on Bioconductor

Man pages

combineBiclusts-methods
Combine two or more Biclust objects into one
discretize
Discretize expression matrix for qualitative biclustering
eSetDimName
Get dimname from an eSet object
fcFilter
Feature-Condition Filter
fcFilter-methods
Feature-Condition Filter
features-methods
Extract features and conditions
generateSeeds-methods
Generate seeds for biclustering
parseQubicBlocks
Parse QUBIC Command Line Tool Output Files
QUBICBiclusterSet-class
Class "QUBICBiclusterSet"
quBicluster
Qualitative Biclustering
readBiclusterResults
Import bicluster results from plain text files
rqubic-package
Qualitative biclustering algorithm for expression data...
writeQubicInputFile
Write an ExpressionSet object into the file format required...

Files in this package

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