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Pvclust specifications

Information


Unique identifier OMICS_19442
Name Pvclust
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
Requirements
parallel, MASS, R(≥2.10.0)
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 <>

Publication for Pvclust

Pvclust in pipelines

 (43)
2018
PMCID: 5765558
PMID: 29319806
DOI: 10.1093/gbe/evx271

[…] present in greater than two genomes. this distance matrix was used for complete linkage hierarchical clustering. to assess the uncertainty in the hierarchical cluster analysis, we used the r package pvclust 2.0-0 () with 10,000 bootstraps. canonical (constrained) correspondence analysis as implemented in canoco 5 () was used to investigate which variables (i.e., membership of the pseudovibrio […]

2018
PMCID: 5774689
PMID: 29351308
DOI: 10.1371/journal.pone.0190933

[…] co-expression network analysis (wgcna) []. gene cluster 3.0 was also utilized to group the degs as different expression patterns during the whole developmental process []. the r package component, pvclust, was utilized to assess the uncertainty in the hierarchical clustering analysis on 10,000 bootstrap replicates []., functional annotations and pathway analyses of degs were carried out using […]

2018
PMCID: 5783949
PMID: 29367672
DOI: 10.1038/s41467-017-02107-w

[…] and the first component coordinates were used to generate the three-dimension graph., heatmaps were drawn with the library complexheatmap with z-score of expression. cluster trees were computed with pvclust with correlation method as distance calculation and ward criteria as construction method., for expression profile of kegg pathways, genes were ordered per fold changes., topgo was used […]

2018
PMCID: 5797686
PMID: 29441023
DOI: 10.3389/fphys.2018.00019

[…] california usa, www.graphpad.com., cel files were analyzed with rstudio (rstudio team, ) (version 0.99.903), r (r development core team, ) (version 3.2.5) and various r-packages (e.g., “affy,” “pvclust,” “gplots,” and “factominer”). for a complete list of the packages including version numbers and citations, please refer to supplement ., pathway analysis was carried out with cluego (bindea […]

2018
PMCID: 5807776
PMID: 29426285
DOI: 10.1186/s12864-018-4505-4

[…] categories. the ratios of the 20 tsp were used as input for hierarchical clustering of the samples, and the robustness of the clusters was calculated using 5000 randomizations with the r package “pvclust” []., additional file 1: additional file 2: , electronic supplementary material , the online version of this article (10.1186/s12864-018-4505-4) contains supplementary material, […]


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Pvclust in publications

 (400)
PMCID: 5942634
PMID: 29768530
DOI: 10.1590/0074-02760170385

[…] of 0.95. the different codon preferences between zikv lineages were independently confirmed by high support values (> 80%) obtained from hierarchical clustering analysis, using the r-package pvclust v1.32 (http://stat.sys.i.kyoto-u.ac.jp/prog/pvclust/). we also investigated the differences in codon preferences between zikv lineages, employing a pca in codon counts, which were calculated […]

PMCID: 5943259
PMID: 29743510
DOI: 10.1038/s41598-018-25434-4

[…] uniprot kb (http://www.uniprot.org/) and kindly made available by nicolas lapalu (l’institut national de la recherché argonomique, versailles, france). clustering analyses were performed using the pvclust package in r studio (https://cran.r-project.org/web/packages/pvclust/index.html) for hierarchical clustering and the deseq package in r studio for principle component analysis clustering, […]

PMCID: 5929417
PMID: 29731974
DOI: 10.18632/oncotarget.24800

[…] to compute the distances between clusters. the mirnas with fdr < 0.05 were defined as statistically significant. bootstrap resampling was used to generate probability values as implemented in pvclust []., pathway analysis of mirnas was performed with diana-mirpath v3.0 software available from http://snf-515788.vm.okeanos.grnet.gr/ []. the diana-tarbase v7.0 was selected as the mirnatarget […]

PMCID: 5951639
PMID: 29655704
DOI: 10.1016/j.cels.2018.03.012

[…] percentages of the maximal heights of the resulting dendrogram. bootstrap analysis to assess cluster stability was performed using the “approximately unbiased” method contained in the r package ‘pvclust’ (, ). the average bootstrap value was computed as the mean of bootstraps for branch points above and below the 60% cut line. for , connectivity profiles were limited to the set […]

PMCID: 5894969
PMID: 29641531
DOI: 10.1371/journal.pone.0194729

[…] in the comparisons for α-diversity indices. β-diversity was assessed using jensen-shannon divergence (jsd) distance matrix. to examine the bacterial community profiles in paired samples, we used “pvclust” r package to perform hierarchical cluster analysis via function “hclust” and calculate the probability value (approximately unbiased [au] p-value) for each cluster using bootstrap analysis […]


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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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