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

Suzuki R; Shimodaira H

doi:10.1093/bioinformatics/btl117

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

Suzuki R ¹,

Shimodaira H

Affiliations

1. Department of Mathematical and Computing Sciences, Tokyo Institute of Technology 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8552, Japan.
Authors
Suzuki R¹
(1 author)

ORCIDs linked to this article

Bioinformatics (Oxford, England), 04 Apr 2006, 22(12):1540-1542
https://doi.org/10.1093/bioinformatics/btl117 PMID: 16595560

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 addition the computation time can be enormously decreased with parallel computing option.

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References

Articles referenced by this article (7)

Bootstrap confidence levels for phylogenetic trees.
Efron B, Halloran E, Holmes S
Proc Natl Acad Sci U S A, (23):13429-13434 1996
MED: 8917608
CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP.
Felsenstein J
Evolution, (4):783-791 1985
MED: 28561359
Diversity of gene expression in adenocarcinoma of the lung.
Garber ME, Troyanskaya OG, Schluens K, Petersen S, Thaesler Z, Pacyna-Gengelbach M, van de Rijn M, Rosen GD, Perou CM, Whyte RI, Altman RB, Brown PO, Botstein D, Petersen I
Proc Natl Acad Sci U S A, (24):13784-13789 2001
MED: 11707590
Bootstrapping cluster analysis: assessing the reliability of conclusions from microarray experiments.
Kerr MK, Churchill GA
Proc Natl Acad Sci U S A, (16):8961-8965 2001
MED: 11470909
CONSEL: for assessing the confidence of phylogenetic tree selection.
Shimodaira H, Hasegawa M
Bioinformatics, (12):1246-1247 2001
MED: 11751242
An approximately unbiased test of phylogenetic tree selection.
Shimodaira H
Syst Biol, (3):492-508 2002
MED: 12079646
Title not supplied
AUTHOR UNKNOWN
ANN STAT 2004

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

Affiliations

Authors

ORCIDs linked to this article

Abstract

Summary

Full text links

References

Bootstrap confidence levels for phylogenetic trees.

CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP.

Diversity of gene expression in adenocarcinoma of the lung.

Bootstrapping cluster analysis: assessing the reliability of conclusions from microarray experiments.

CONSEL: for assessing the confidence of phylogenetic tree selection.

An approximately unbiased test of phylogenetic tree selection.

Title not supplied

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Citations of article over time

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Smart citations by scite.ai
Explore citation contexts and check if this article has been supported or disputed.
https://scite.ai/reports/10.1093/bioinformatics/btl117

Article citations

Diversity, composition and potential roles of sedimentary microbial communities in different coastal substrates around subtropical Okinawa Island, Japan.

Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake.

Mutations in glioblastoma proteins do not disrupt epitope presentation and recognition, maintaining a specific CD8 T cell immune response potential.

Single-cell resolution characterization of myeloid-derived cell states with implication in cancer outcome.

Transcriptional immune suppression and up-regulation of double-stranded DNA damage and repair repertoires in ecDNA-containing tumors.

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Search life-sciences literature (44,689,181 articles, preprints and more)

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

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