articleBioinformaticsApr 4, 2006BRONZE OA

Pvclust: an R package for assessing the uncertainty in hierarchical clustering

RSRyota SuzukiHSHidetoshi Shimodaira

Tokyo Institute of Technology

PubMed
Indexed incrossrefdoajpubmed

Abstract

Abstract Summary: Pvclust is an add-on package for a statistical software R to assess the uncertainty in hierarchical cluster analysis. Pvclust can be used easily for general statistical problems, such as DNA microarray analysis, to perform the bootstrap analysis of clustering, which has been popular in phylogenetic analysis. Pvclust calculates probability values (p-values) for each cluster using bootstrap resampling techniques. Two types of p-values are available: approximately unbiased (AU) p-value and bootstrap probability (BP) value. Multiscale bootstrap resampling is used for the calculation of AU p-value, which has superiority in bias over BP value calculated by the ordinary bootstrap resampling. In…

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Topics & keywords

Topics
Keywords
  • Resampling
  • R package
  • Computer science
  • Cluster analysis
  • Permutation (music)
  • Hierarchical clustering
  • MIT License
  • Computation
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