QUBIC: An R package for qualitative biclustering in support of gene co-expression analyses

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).

Package details

AuthorYu Zhang [aut, cre], Qin Ma [aut]
Bioconductor views Clustering DifferentialExpression GeneExpression Microarray MultipleComparison Network StatisticalMethod Visualization
MaintainerYu Zhang <[email protected]>
LicenseCC BY-NC-ND 4.0 + file LICENSE
URL http://github.com/zy26/QUBIC
Package repositoryView on Bioconductor
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QUBIC documentation built on Nov. 1, 2018, 2:23 a.m.