rqubic: Qualitative biclustering algorithm for expression data analysis in R
Version 1.22.0

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

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
Version1.22.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("rqubic")

Getting started

Package overview

Popular man pages

combineBiclusts-methods: Combine two or more Biclust objects into one
eSetDimName: Get dimname from an eSet object
fcFilter: Feature-Condition Filter
features-methods: Extract features and conditions
parseQubicBlocks: Parse QUBIC Command Line Tool Output Files
readBiclusterResults: Import bicluster results from plain text files
writeQubicInputFile: Write an ExpressionSet object into the file format required...
See all...

All man pages Function index File listing

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...

Functions

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
rqubic documentation built on May 20, 2017, 10:28 p.m.

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