ShrinkBayes: a versatile R-package for analysis of count-based sequencing data in complex study designs

M.A. van de Wiel, M. Neerincx, T.E. Buffart, D.L.S. Sie, H.M. Verheul

    Research output: Contribution to JournalArticleAcademicpeer-review


    Background: Complex designs are common in (observational) clinical studies. Sequencing data for such studies are produced more and more often, implying challenges for the analysis, such as excess of zeros, presence of random effects and multi-parameter inference. Moreover, when sample sizes are small, inference is likely to be too liberal when, in a Bayesian setting, applying a non-appropriate prior or to lack power when not carefully borrowing information across features.Results: We show on microRNA sequencing data from a clinical cancer study how our software ShrinkBayes tackles the aforementioned challenges. In addition, we illustrate its comparatively good performance on multi-parameter inference for groups using a data-based simulation. Finally, in the small sample size setting, we demonstrate its high power and improved FDR estimation by use of Gaussian mixture priors that include a point mass.Conclusion: ShrinkBayes is a versatile software package for the analysis of count-based sequencing data, which is particularly useful for studies with small sample sizes or complex designs. © 2014 van de Wiel et al.; licensee BioMed Central Ltd.
    Original languageEnglish
    Article number116
    Pages (from-to)116
    JournalBMC Bioinformatics
    Publication statusPublished - 2014


    Dive into the research topics of 'ShrinkBayes: a versatile R-package for analysis of count-based sequencing data in complex study designs'. Together they form a unique fingerprint.

    Cite this