Pvclust protocols

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description
Pvclust computational protocol

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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Documentation


Maintainers


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

Publication for Pvclust

Pvclust IN pipelines

 (10)
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 (suzuki and shimodaira 2006) with 10,000 bootstraps. canonical (constrained) correspondence analysis as implemented in canoco 5 (šmilauer and lepš 2014) was used to investigate […]

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

[…] network analysis (wgcna) [20]. gene cluster 3.0 was also utilized to group the degs as different expression patterns during the whole developmental process [21]. the r package component, pvclust, was utilized to assess the uncertainty in the hierarchical clustering analysis on 10,000 bootstrap replicates [22]., functional annotations and pathway analyses of degs were carried […]

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” [79]., additional file 1: additional file 2: , electronic supplementary material , the online version of this article (10.1186/s12864-018-4505-4) contains supplementary material, […]

2016
PMCID: 5054979
PMID: 27525369
DOI: 10.1038/ni.3533

[…] 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 […]

2016
PMCID: 5464975
PMID: 27991934
DOI: 10.1038/onc.2016.471

[…] cuffdiff.51 r (r core team 2013) was used to visualize expression data. genes with rnaseq expression variation over 0.2 were log transformed and mean centered. the resulting data was clustered using pvclust package with correlation as distance metric and average clustering method.52 differential transcript expression was defined using a benjamini–hochberg-corrected q-value of ⩽0.01. the data […]

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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