Package: QUBIC
Type: Package
Title: An R package for qualitative biclustering in support of gene
        co-expression analyses
Description: 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).
Authors@R: c(person("Yu", "Zhang", role = c("aut", "cre"), email = "zy26@jlu.edu.cn"),
             person("Qin", "Ma", role = "aut", email = "qin.ma@sdstate.edu"))
VignetteBuilder: knitr
biocViews: StatisticalMethod, Microarray, DifferentialExpression,
        MultipleComparison, Clustering, Visualization, GeneExpression,
        Network
Version: 1.38.0
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
Config/pak/sysreqs: libicu-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:31:14 UTC
RemoteUrl: https://github.com/bioc/QUBIC
RemoteRef: RELEASE_3_22
RemoteSha: d4c6579c9ae5097f7cfa38c8d5cb83c7fd8c0c0a
NeedsCompilation: yes
Packaged: 2025-12-22 08:56:09 UTC; root
Author: Yu Zhang [aut, cre],
  Qin Ma [aut]
Maintainer: Yu Zhang <zy26@jlu.edu.cn>
Built: R 4.5.2; x86_64-w64-mingw32; 2025-12-22 08:57:51 UTC; windows
Archs: x64
