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hierarchicalSets specifications


Unique identifier OMICS_20170
Name hierarchicalSets
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A presence–absence matrix with sets as columns and elements as rows, or a list of sets defined by their elements
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 1.0.2
Stability Stable
methods, stats, RColorBrewer, Matrix, utils, grDevices, Rcpp, scales, MASS, R(≥3.2.0), gtable, ggplot2(≥2.0.0), ggdendro
Source code URL https://cran.r-project.org/src/contrib/hierarchicalSets_1.0.2.tar.gz
Maintained Yes




No version available



  • person_outline Thomas Lin Pedersen <>

Publication for hierarchicalSets

hierarchicalSets citation


Updating the genomic taxonomy and epidemiology of Campylobacter hyointestinalis

PMCID: 5799301
PMID: 29403020
DOI: 10.1038/s41598-018-20889-x

[…] hmmer3 (http://hmmer.janelia.org/) to query bactnog, the bacterial subset of the eggnog4.5 database through the online eggnog-mapper tool. pangenome composition was explored and visualised using the hierarchicalsets package in r. tanglegrams were generated using the dendextend package for r. gene gain and loss events were estimated using the count software package based on the birth and death […]

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hierarchicalSets institution(s)
Department of Systems Biology, Center for Biological Sequence Analysis, The Technical University of Denmark, Lyngby, Denmark; Assays, Culture and Enzymes Division, Hørsholm, Denmark
hierarchicalSets funding source(s)
Supported by The Danish Agency for Science, Technology and Innovation.

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