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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 (3.19)

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 (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Clustering, DifferentialExpression, GeneExpression, Microarray, MultipleComparison, Network, Software, StatisticalMethod, Visualization
Version 1.31.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License CC BY-NC-ND 4.0 + file LICENSE
Depends R (>= 3.1), biclust
Imports Rcpp (>= 0.11.0), methods, Matrix
System Requirements C++11, Rtools (>= 3.1)
URL http://github.com/zy26/QUBIC
Bug Reports http://github.com/zy26/QUBIC/issues
See More
Suggests QUBICdata, qgraph, fields, knitr, rmarkdown
Linking To Rcpp, RcppArmadillo
Enhances RColorBrewer
Depends On Me
Imports Me mosbi
Suggests Me runibic
Links To Me
Build Report Build Report

Package Archives

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

Source Package QUBIC_1.31.0.tar.gz
Windows Binary QUBIC_1.31.0.zip
macOS Binary (x86_64) QUBIC_1.31.0.tgz
macOS Binary (arm64) QUBIC_1.31.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/QUBIC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/QUBIC
Bioc Package Browser https://code.bioconductor.org/browse/QUBIC/
Package Short Url https://bioconductor.org/packages/QUBIC/
Package Downloads Report Download Stats