To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("QUBIC")
In most cases, you don't need to download the package archive at all.
QUBIC
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An R package for qualitative biclustering in support of gene co-expression analyses
Bioconductor version: Release (3.4)
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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("QUBIC")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("QUBIC")
| R Script | QUBIC Tutorial | |
| Reference Manual | ||
| Text | NEWS | |
| Text | LICENSE |
Details
| biocViews | Clustering, DifferentialExpression, GeneExpression, Microarray, MultipleComparison, Network, Software, StatisticalMethod, Visualization |
| Version | 1.2.1 |
| In Bioconductor since | BioC 3.3 (R-3.3) (1 year) |
| 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 |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | QUBIC_1.2.1.tar.gz |
| Windows Binary | QUBIC_1.2.1.zip (32- & 64-bit) |
| Mac OS X 10.9 (Mavericks) | QUBIC_1.2.1.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/QUBIC/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/QUBIC/ |
| Package Downloads Report | Download Stats |
Documentation »
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