QUBIC
An R Package for Qualitative Biclustering in Support of Gene Co-Expression Analyses
Bioconductor version: 3.24 · Package version: 1.41.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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).
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("QUBIC")Details
| Maintainer | Yu Zhang <zy26@jlu.edu.cn> |
| Author | Yu Zhang [aut, cre], Qin Ma [aut] |
| License | CC BY-NC-ND 4.0 + file LICENSE |
| URL | https://github.com/zy26/QUBIC |
| Bug Reports | https://github.com/zy26/QUBIC/issues |
| System Requirements | C++11, Rtools (>= 3.1) |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Clustering, DifferentialExpression, GeneExpression, Microarray, MultipleComparison, Network, Software, StatisticalMethod, Visualization |
| Package Short Url | https://bioconductor.org/packages/QUBIC/ |
Citation
From within R, enter citation("QUBIC"):
Yu Zhang, Qin Ma. QUBIC: An R Package for Qualitative Biclustering in Support of Gene Co-Expression Analyses. doi:10.18129/B9.bioc.QUBIC, R package version 1.41.0, https://bioconductor.org/packages/QUBIC.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | QUBIC_1.41.0.tar.gz |
| Windows binary (x86_64) | QUBIC_1.41.0.zip |
| macOS binary (arm64) | QUBIC_1.41.0.tgz |
| macOS binary (x86_64) | QUBIC_1.41.0.tgz |
Dependencies
Depends: R (>= 4.5.0)
Imports: Rcpp (>= 0.11.0), methods, Matrix
LinkingTo: Rcpp, RcppArmadillo
Suggests: QUBICdata, qgraph, fields, knitr, rmarkdown
Enhances: RColorBrewer