QUBIC2

QUBIC2 is a biclustering algorithm to detect condition-specific functional gene modules (biclusters) in large-scale gene expression data, particularly in RNA-Sequencing (RNA-Seq) and single-cell RNA-Seq (scRNA-Seq) data. It addresses existing methods' limitations by comprehensively detecting all significant bicluster structures and handling the challenges posed by massive zero and low expression values in RNA-Seq data.

Key features of QUBIC2 include:

1. A novel left-truncated mixture of Gaussian model for accurately assessing multimodality in zero-enriched expression data.

2. A fast and efficient dropouts-saving expansion strategy for functional gene modules optimization using information divergency.

3. A rigorous statistical test for the significance of all identified biclusters, even in organisms with limited functional annotations.

Topic

RNA-Seq;Microarray experiment;Gene expression

Detail

  • Operation: Enrichment analysis

  • Software interface: Command-line user interface

  • Language: C++

  • License: Not stated

  • Cost: Free of charge

  • Version name: -

  • Credit: The National Institute of General Medical Sciences of the National Institutes of Health, and the Extreme Science and Engineering Discovery Environment, which is supported by the National Science Foundation.

  • Input: -

  • Output: -

  • Contact: Chi Zhang czhang87@iu.edu, Qin Ma qin.ma@osumc.edu

  • Collection: -

  • Maturity: -

Publications

  • QUBIC2: a novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data.
  • Xie J, et al. QUBIC2: a novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data. QUBIC2: a novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data. 2020; 36:1143-1149. doi: 10.1093/bioinformatics/btz692
  • https://doi.org/10.1093/bioinformatics/btz692
  • PMID: 31503285
  • PMC: PMC8215922

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