Hclust pipeline

Hclust specifications

Information


Unique identifier OMICS_25363
Name Hclust
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 1.06
Stability Stable
Requirements matplotlib, numpy, scipy
Maintained Yes

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Maintainer


  • person_outline Mark A. Ragan <>

Publication for Hclust

Hclust IN pipelines

 (6)
2018
PMCID: 5884486
PMID: 29617380
DOI: 10.1371/journal.pone.0193515

[…] with similar names and overlapping content, the smallest pathway was removed. this led to 36 pathways being excluded. on the remaining 424 pathways we performed a cluster analysis in r using the “hclust” function with euclidean distance and complete linkage clustering. we obtained 81 clusters of pathways and 36 individual pathways. we displayed the resulting 117 pathway clusters as a network […]

2018
PMCID: 5906602
PMID: 29670130
DOI: 10.1038/s41598-018-24425-9

[…] pathway topologies, comprised of genes and their directional interactions, are obtained from the kegg database79., the hierarchical clustering and venn plot were carried out using rpudplus, hclust and venn diagram function in r-studio employing differentially expressed pre-ranked genes which were associated with extracellular secretory function as classified using topgo r-studio package […]

2013
PMCID: 3855576
PMID: 24340035
DOI: 10.1371/journal.pone.0082516

[…] sample (sample 45_abdominal) all samples showed good quality and could be used for further analysis. unsupervised hierarchical clustering (euclidean distance) was performed using the function hclust of the r statistical package. to identify genes differentially expressed in abdominal and gluteal fat samples, the limma package [19] for the r statistical software was used to compute […]

2012
PMCID: 3281076
PMID: 22359580
DOI: 10.1371/journal.pone.0031241

[…] the r “e1071” package was used for support vector machine (svm) with the non-linear radial basis function as the kernel. the unsupervised hierarchical clustering algorithm was implemented in the r “hclust” function and generated using euclidean distance matrix and complete-linkage agglomeration. all heat maps were generated using the r “gplots” package., mirna biomarker selection: biomarker […]

2011
PMCID: 3296464
PMID: 21852250
DOI: 10.1093/gbe/evr069

[…] on genes with p < 0.05 and fc > 1.5. individuals and genes were clustered with pearson correlation index and spearman correlation index, respectively. dendograms were drawn using the “hclust” function in r script., to identify major themes appearing among the differentially expressed genes, we used the software blast2go (conesa et al. 2005; götz et al. 2008) to test […]

Hclust institution(s)
University of Queensland, Institute for Molecular Bioscience, Brisbane, QLD, Australia; Australian Research Council Centre of Excellence in Bioinformatics, University of Queensland, Institute for Molecular Bioscience, St Lucia, QLD, Australia
Hclust funding source(s)
Supported by Australian Research Council (DP110103384 and CE034822).

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