QUBIC: An R package for qualitative biclustering in support of gene co-expression analyses
Version 1.4.0

The core function of this R package is to provide the implementation of the well-cited and well-reviewed QUBIC algorithm, aiming to deliver an effective and efficient biclustering capability. This package also includes the following related functions: (i) a qualitative representation of the input gene expression data, through a well-designed discretization way considering the underlying data property, which can be directly used in other biclustering programs; (ii) visualization of identified biclusters using heatmap in support of overall expression pattern analysis; (iii) bicluster-based co-expression network elucidation and visualization, where different correlation coefficient scores between a pair of genes are provided; and (iv) a generalize output format of biclusters and corresponding network can be freely downloaded so that a user can easily do following comprehensive functional enrichment analysis (e.g. DAVID) and advanced network visualization (e.g. Cytoscape).

Browse man pages Browse package API and functions Browse package files

AuthorYu Zhang [aut, cre], Qin Ma [aut]
Bioconductor views Clustering DifferentialExpression GeneExpression Microarray MultipleComparison Network StatisticalMethod Visualization
Date of publicationNone
MaintainerYu Zhang <zy26@jlu.edu.cn>
LicenseCC BY-NC-ND 4.0 + file LICENSE
Version1.4.0
URL http://github.com/zy26/QUBIC
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("QUBIC")

Man pages

BCQU-class: Class BCQU.
QUBIC: QUBIC: A Qualitative Biclustering Algorithm for Analyses of...
qudiscretize: Create a qualitative discrete matrix for a given gene...
quheatmap: Visualization of identified biclusters
qunet2xml: Convert newwork to XGMML
qunetwork: Construction and visualization of co-expression network
showinfo: Show report of biclusters

Functions

BCQU Man page Man page Source code
BCQU-class Man page
BCQUD Man page Source code
BCQUD-class Man page
QUBIC Man page
QUBICD Man page
QUD Man page
Qnetwork Man page
Qunetwork Man page
bcqu Man page
biclust,matrix,BCQU-method Man page
biclust,matrix,BCQUD-method Man page
network Man page
qdiscretize Man page
qubic Man page
qubic_d Man page Source code
qubic_de Source code
qubic_dw Source code
qubiclust Man page Source code
qubiclust_d Man page Source code
qudiscretize Man page Source code
quheatmap Man page Source code
qunet2xml Man page Source code
qunetwork Man page Source code
showinfo Man page Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
R
R/RcppExports.R
R/aaa-qubic.R
R/qubiclust.R
R/quheatmap.R
R/qunet2xml.R
R/qunetwork.R
R/showinfo.R
build
build/vignette.rds
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/qubic_vignette.R
inst/doc/qubic_vignette.Rmd
inst/doc/qubic_vignette.pdf
man
man/BCQU-class.Rd
man/QUBIC.Rd
man/qudiscretize.Rd
man/quheatmap.Rd
man/qunet2xml.Rd
man/qunetwork.Rd
man/showinfo.Rd
src
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/block.h
src/charset.cc
src/charset.h
src/cluster.cc
src/cluster.h
src/config.h
src/discrete.h
src/discretize.cc
src/discretize.h
src/edge_list.cc
src/edge_list.h
src/fib.c
src/fib.h
src/fibpriv.h
src/fopen_matrix.cc
src/fopen_matrix.h
src/fstream_matrix.h
src/matrix.h
src/matrix_float.h
src/option.h
src/qubic.cc
src/qubic.h
src/rcpp_qubic.cpp
src/struct.cc
src/struct.h
src/version.h
vignettes
vignettes/bibliography.bib
vignettes/qubic_vignette.Rmd
QUBIC documentation built on May 20, 2017, 9:13 p.m.