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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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Versioning


No version available

Maintainer


  • person_outline Mark A. Ragan

Publication for Hclust

Hclust citations

 (426)
call_split

Dramatic dysbalancing of the Wnt pathway in breast cancers

2018
Sci Rep
PMCID: 5943245
PMID: 29743726
DOI: 10.1038/s41598-018-25672-6
call_split See protocol

[…] s using scripts developed in R (using packages Hmisc and gplots) and export pairwise correlation data in Cytoscape for building the networks. The complete linkage algorithm in the built-in R function hclust has been used to create dendrogram and identify major clusters of the genes in all cases.To confirm the validity of the correlation networks we have identified, Supplementary Fig.  shows compar […]

library_books

Effects of habitat suitability for vectors, environmental factors and host characteristics on the spatial distribution of the diversity and prevalence of haemosporidians in waterbirds from three Brazilian wetlands

2018
PMCID: 5930942
PMID: 29716645
DOI: 10.1186/s13071-018-2847-z

[…] ce probability among colonies. All analyses were performed in R software [] using the vegan package [] and the commands decostant (standardise), dist (distance matrix based on Euclidean distance) and hclust (based on average). […]

call_split

High Rate of Infection by Only Oncogenic Human Papillomavirus in Amerindians

2018
PMCID: 5932372
PMID: 29720524
DOI: 10.1128/mSphere.00176-18
call_split See protocol

[…] likelihood method was used in PhyMLb (). The tree was rooted with theta HPV type (not shown in the figure) ( and ). The hierarchical tree for HPV and urban groups or individual women was built using hclust function from the R base “stats” package by the Spearman method and was visualized together with a heat map plotted with heatmap.2 from gplots () and RColorBrewer () from R packages.Alpha and g […]

call_split

Toll like receptors mediated pathways activate inflammatory responses in the esophageal mucosa of adult eosinophilic esophagitis

2018
PMCID: 5915448
PMID: 29691386
DOI: 10.1038/s41424-018-0017-4
call_split See protocol

[…] sing Singular Value Decomposition (SVD) with imputation. Heatmap is plotted using pheatmap R package (version 0.7.7). The package uses popular clustering distances and methods implemented in dist and hclust functions in R. Heatmaps show a data matrix where coloring gives an overview of the numeric differences, and genes and samples are clustered hierarchically. […]

library_books

Bifidobacteria isolated from vaginal and gut microbiomes are indistinguishable by comparative genomics

2018
PLoS One
PMCID: 5912743
PMID: 29684056
DOI: 10.1371/journal.pone.0196290

[…] scores (tetra) within JSpecies []. ANIm values were visualized as heatmap, generated in R. The ‘vegdist’ function was used to calculate the Euclidean distance between the ANI divergence values, and ‘hclust’ function was used to calculate the complete linkage on the distance matrix, in R.CSI Phylogeny was used to call SNPs (single-nucleotide polymorphisms) and infer phylogeny based on the concaten […]

library_books

Integrative bioinformatics analysis characterizing the role of EDC3 in mRNA decay and its association to intellectual disability

2018
BMC Med Genomics
PMCID: 5914069
PMID: 29685133
DOI: 10.1186/s12920-018-0358-6

[…] A-seq and microarray experiments from ArrayExpress []. Tissue expression profiles of DEGs with an associated HGNC symbol could be extracted from the Atlas and clustered using hierarchical clustering (hclust function in R/Bioconductor).For analyses on a protein level a human protein-protein interaction network (PPI) published by Li et al. [] was employed. This network was based on interactions cont […]

Citations

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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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