QUBIC
An R package for qualitative biclustering in support of gene co-expression analyses
Bioconductor version: Release (3.17)
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("QUBIC")):
Installation
To install this package, start R (version "4.3") 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")| QUBIC Tutorial | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, DifferentialExpression, GeneExpression, Microarray, MultipleComparison, Network, Software, StatisticalMethod, Visualization |
| Version | 1.28.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (7.5 years) |
| License | CC BY-NC-ND 4.0 + file LICENSE |
| Depends | R (>= 3.1), biclust |
| Imports | Rcpp (>= 0.11.0), methods, Matrix |
| Linking To | Rcpp, RcppArmadillo |
| Suggests | QUBICdata, qgraph, fields, knitr, rmarkdown |
| System Requirements | C++11, Rtools (>= 3.1) |
| Enhances | RColorBrewer |
| URL | http://github.com/zy26/QUBIC |
| Bug Reports | http://github.com/zy26/QUBIC/issues |
See More
| 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_1.28.0.tar.gz |
| Windows Binary | QUBIC_1.28.0.zip |
| macOS Binary (x86_64) | QUBIC_1.28.0.tgz |
| macOS Binary (arm64) | QUBIC_1.28.0.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 |