QUBIC

QUBIC is a biclustering program widely utilized for identifying co-expressed genes within subsets of conditions in large-scale transcriptomic datasets. This abstract introduces an R implementation of QUBIC with notable enhancements: (i) an 82% average improvement in efficiency through source code refactoring and optimization and (ii) a comprehensive set of functions facilitating various aspects of biclustering-based biological studies. These functions include qualitative representation (discretization) of expression data, query-based biclustering, bicluster expansion, comparison of biclusters, heatmap visualization for identified biclusters, and elucidating co-expression networks.

Topic

Gene expression

Detail

  • Operation: Gene expression clustering

  • Software interface: Command-line user interface;Library

  • Language: R

  • License: CC-BY-NC-ND-4.0 + file LICENSE

  • Cost: Free

  • Version name: 1.26.0

  • Credit: State of South Dakota Research Innovation Center, the Agriculture Experiment Station of South Dakota State University, National Science Foundation of United States, the National Natural Science Foundation of China.

  • Input: -

  • Output: -

  • Contact: Yu Zhang zy26@jlu.edu.cn

  • Collection: -

  • Maturity: Stable

Publications

  • QUBIC: a bioconductor package for qualitative biclustering analysis of gene co-expression data.
  • Zhang Y, et al. QUBIC: a bioconductor package for qualitative biclustering analysis of gene co-expression data. QUBIC: a bioconductor package for qualitative biclustering analysis of gene co-expression data. 2017; 33:450-452. doi: 10.1093/bioinformatics/btw635
  • https://doi.org/10.1093/bioinformatics/btw635
  • PMID: 28172469
  • PMC: -

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