Pvclust specifications

Information


Unique identifier OMICS_19442
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Advanced
Version 2.0-0
Stability Stable
Source code URL https://cran.r-project.org/src/contrib/pvclust_2.0-0.tar.gz
Maintained Yes

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Maintainers


  • person_outline Ryota Suzuki <>
  • person_outline Hidetoshi Shimodaira <>
  • person_outline Ryota Suzuki <>

Pvclust article

Pvclust citations

 (5)
2016
PMCID: 5054979

[…] cluster analysis was performed using the top 15,000 probes with highest variance across all samples (euclidean distance and ward’s criterion). to assess the uncertainty in cluster analysis, we run pvclust r package with 5,000 bootstrap resampling27. to identify genes whose expression was specifically high in one b cell subset compared to others, we performed a student’s t-test (p < 0.05 […]

2015
PMCID: 4860271

[…] gene symbol, or affymetrix probeset id. profiles were made using the ggplot2 (wickham 2009) package in r (r core development team 2008)., cluster analysis and bootstrapping were performed using the pvclust package (suzuki and shimodaira 2006). for each probeset, average log2 signal intensity was calculated for each time point, and these data were analyzed using the pvclust function […]

2013
PMCID: 3920955

[…] genes with student's t-test p-values<0.05 with a fold-change of >1.5 (figure 5a). hierarchical clustering with pearson's correlation of the degs was analyzed using r software (bioconductor, pvclust). statistically enriched signaling pathways of clustered degs were ranked and categorized according to kegg pathway using david 6.7 software.57 gene interaction network between the clustered […]

2012
PMCID: 3353902

[…] average-linkage method. the robustness of sample clusters was evaluated via multiscale bootstrapping (1000 replicates) using the approximately unbiased (au) method as implemented using the program pvclust in the r language [26], [27]., the proportion of differentially expressed (de) genes between samples was estimated via an empirical bayesian approach in the r program bayseq [28]. posterior […]

2012
PMCID: 3250443

[…] files were quantified with the dfw [9] using statistical language r (http://www.r-project) [33] and bioconductor (http://www.bioconductor.org/) [34]. hierarchical clustering was performed using the pvclust() function [35] in r. to identify degs, the rp method [10] was applied to dfw quantified data, with the number of permutations set at 1,000. probe sets with an fdr <0.05 were regarded […]

Pvclust institution(s)
Department of Mathematical and Computing Sciences, Tokyo Institute of Technology, Tokyo, Japan; Ef-prime, Inc., Tokyo, Japan
Pvclust funding source(s)
Supported in part by Grant KAKENHI (14702061, 17700276) from MEXT of Japan.

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