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Bioconductor - QUBIC (development version)

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 (3.22)

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 "4.5") 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")
Details biocViews Clustering, DifferentialExpression, GeneExpression, Microarray, MultipleComparison, Network, Software, StatisticalMethod, Visualization Version 1.37.0 In Bioconductor since BioC 3.3 (R-3.3) (9 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 Package Archives

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

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