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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, DifferentialExpression, GeneExpression, Microarray, MultipleComparison, Network, Software, StatisticalMethod, Visualization |
| Version | 1.41.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10.5 years) |
| License | CC BY-NC-ND 4.0 + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | Rcpp (>= 0.11.0), methods, Matrix |
| System Requirements | C++11, Rtools (>= 3.1) |
| URL | https://github.com/zy26/QUBIC |
| Bug Reports | https://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_1.41.0.tar.gz |
| Windows Binary (x86_64) | QUBIC_1.41.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | QUBIC_1.41.0.tgz |
| macOS Binary (sonoma-arm64) | QUBIC_1.41.0.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 |