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]|
|Date of publication||None|
|Maintainer||Yu Zhang <firstname.lastname@example.org>|
|License||CC BY-NC-ND 4.0 + file LICENSE|
BCQU-class: Class BCQU.
QUBIC: QUBIC: A Qualitative Biclustering Algorithm for Analyses of...
qudiscretize: Create a qualitative discrete matrix for a given gene...
quheatmap: Visualization of identified biclusters
qunet2xml: Convert newwork to XGMML
qunetwork: Construction and visualization of co-expression network
showinfo: Show report of biclusters