To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("QUBIC")

In most cases, you don't need to download the package archive at all.

QUBIC

DOI: 10.18129/B9.bioc.QUBIC    

This is the development version of QUBIC; for the stable release version, see QUBIC.

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

Bioconductor version: Development (3.6)

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).

Author: Yu Zhang [aut, cre], Qin Ma [aut]

Maintainer: Yu Zhang <zy26 at jlu.edu.cn>

Citation (from within R, enter citation("QUBIC")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("QUBIC")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("QUBIC")

 

PDF R Script QUBIC Tutorial
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews Clustering, DifferentialExpression, GeneExpression, Microarray, MultipleComparison, Network, Software, StatisticalMethod, Visualization
Version 1.5.0
In Bioconductor since BioC 3.3 (R-3.3) (1.5 years)
License CC BY-NC-ND 4.0 + file LICENSE
Depends R (>= 3.1), biclust
Imports Rcpp (>= 0.11.0), methods, Matrix
LinkingTo Rcpp, RcppArmadillo
Suggests QUBICdata, qgraph, fields, knitr, rmarkdown
SystemRequirements C++11, Rtools (>= 3.1)
Enhances RColorBrewer
URL http://github.com/zy26/QUBIC
BugReports http://github.com/zy26/QUBIC/issues
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package QUBIC_1.5.0.tar.gz
Windows Binary QUBIC_1.5.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) QUBIC_1.5.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/QUBIC
Package Short Url http://bioconductor.org/packages/QUBIC/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: