QUBIC

DOI: 10.18129/B9.bioc.QUBIC    

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

Bioconductor version: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("QUBIC")

For older versions of R, please refer to the appropriate Bioconductor release.

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	1.24.0
In Bioconductor since	BioC 3.3 (R-3.3) (6.5 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	mosbi
Suggests Me	runibic
Links To Me
Build Report

Package Archives

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

Source Package	QUBIC_1.24.0.tar.gz
Windows Binary	QUBIC_1.24.0.zip (64-bit only)
macOS Binary (x86_64)	QUBIC_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/QUBIC
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/QUBIC
Package Short Url	https://bioconductor.org/packages/QUBIC/
Package Downloads Report	Download Stats