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

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).

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("QUBIC")
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
Version1.2.1
http://github.com/zy26/QUBIC

View on Bioconductor

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

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

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.