Hclust protocols

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Hclust specifications


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
matplotlib, numpy, scipy
Maintained Yes



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  • person_outline Mark A. Ragan <>

Publication for Hclust

Hclust in pipelines

PMCID: 5771622
PMID: 29342213
DOI: 10.1371/journal.pone.0191407

[…] multidimensional scaling (mds) using the transcriptomes of each sample in the cummerbund and prcomp packages in r bioconductor under the default settings []. for hierarchical clustering, we used the hclust package in r []. dendrograms were created using ward linkage from z-score normalized transcript levels., we performed gene set enrichment analysis using the open-source software go::termfinder […]

PMCID: 5784595
PMID: 29368634
DOI: 10.1186/s13567-018-0504-3

[…] least two of eight samples were selected for further analysis. genes that were statistically significantly differentially expressed in the two groups were identified with volcano plot filtering. the hclust function (r package stats) was used to perform hierarchical clustering (ward’s method) []. heatmaps were produced with the heatmap.2 function (r package gplots) []., the datasets […]

PMCID: 5819258
PMID: 29458328
DOI: 10.1186/s12861-018-0163-7

[…] of a peak at that promoter for that cell type. for the hierarchical tree of gene expression, the output matrix from cuffnorm command was used. hierarchical clustering was performed using the hclust function from the fastcluster package in r []. the euclidean distance of the columns of each matrix (cell types) was used as a dissimilarity matrix and the method chosen was complete., […]

PMCID: 5886532
PMID: 29621268
DOI: 10.1371/journal.pone.0195102

[…] adonis in vegan were used to identify statistically significant variables. samples were classified into depth groups of surface, abyssal, or hadal by upgma hierarchical clustering using the command hclust. samples were classified based on a hard depth cutoff in each trench; samples that clustered with one depth group but belonged to the other based on depth cutoff were grouped by depth […]

PMCID: 5896245
PMID: 29634948
DOI: 10.1016/j.ccell.2018.03.013

[…] were imputed by adopting the genotypes of the closest related snp, as measured by euclidian distance across the sample set., hierarchical clustering was then performed by applying the default r hclust() function (method: 'complete'), defining each genotype value as follows:(i)homozygous 1/1: 0(ii)heterozygous 1/2: 0.5(iii)homozygous 2/2: 1, homozygous 1/1: 0, heterozygous 1/2: 0.5, […]

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Hclust in publications

PMCID: 5940898
PMID: 29739963
DOI: 10.1038/s41598-018-25086-4

[…] pairwise.perm.manova of the rvaidememoire package for r) were used to evaluate statistically significant differences between the zoantharian species. a hierarchical cluster analysis (function hclust using euclidian distance) was used to identify the similarities between the different zoantharian species. the ‘average’ algorithm was chosen after analysis of the cophenetic correlation […]

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

[…] 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)., the presence of avian haemosporidians in the blood of nestlings was investigated. dna samples extracted from the blood of waterbirds were screened for species […]

PMCID: 5932372
PMID: 29720524
DOI: 10.1128/mSphere.00176-18

[…] 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 […]

PMCID: 5930502
PMID: 29720131
DOI: 10.1186/s12876-018-0785-z

[…] according to the jaccard index [] by mean of the “vegdist” function within the vegan r package. the samples have been then clustered hierarchically according to the upgma method by using the “hclust” function within the stats r package., human peripheral blood mononuclear cells (pbmcs) were isolated by ficoll-hypaque density gradient centrifugation (biochrom, berlin, germany) from buffy […]

PMCID: 5938556
PMID: 29765370
DOI: 10.3389/fmicb.2018.00870

[…] done using the “anosim” function from the vegan package version 2.4-3 (). the rarefied dataset was also used to test similarity between technical replicates with hierarchical clustering using the “hclust” function in r version 3.3.0 of bray–curtis dissimilarities between samples found using the “vegdist” function in vegan., bray–curtis dissimilarities between pig stables and associated […]

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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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