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Dynamic Tree Cut specifications

Information


Unique identifier OMICS_23803
Name Dynamic Tree Cut
Alternative name dynamicTreeCut
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 1.63-1
Stability Stable
Source code URL https://cran.r-project.org/src/contrib/dynamicTreeCut_1.63-1.tar.gz
Maintained No

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Additional information


https://cran.r-project.org/web/packages/dynamicTreeCut/index.html https://cran.r-project.org/web/packages/moduleColor/index.html https://labs.genetics.ucla.edu/horvath/htdocs/CoexpressionNetwork/BranchCutting/InstallationInstructions.html

Publication for Dynamic Tree Cut

Dynamic Tree Cut citations

 (32)
library_books

Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes

2018
Nat Commun
PMCID: 5958058
PMID: 29773832
DOI: 10.1038/s41467-018-04383-6

[…] inary distance and Ward linkage metrics. Clustering of chromatin states regions was performed using hierarchical clustering and the number of clusters was determined using the cutreeDynamic function (dynamicTreeCut R package) with a minimum size module of 500 features. […]

library_books

Gene co expression networks in liver and muscle transcriptome reveal sex specific gene expression in lambs fed with a mix of essential oils

2018
BMC Genomics
PMCID: 5885410
PMID: 29618337
DOI: 10.1186/s12864-018-4632-y

[…] Overlap Measure (TOM) corresponding to the overlap between pairs of interconnected genes [].TOM was used to build a gene clustering dendrogram. Highly interconnected genes were clustered by using the dynamicTreeCut algorithm [] with all the parameters at default values. Each cluster also called “module” was arbitrarily labelled with a unique colour (e.g brown4).Next, for each module a module eigen […]

library_books

ConGEMs: Condensed Gene Co Expression Module Discovery Through Rule Based Clustering and Its Application to Carcinogenesis

2017
Genes
PMCID: 5793160
PMID: 29283433
DOI: 10.3390/genes9010007

[…] the integrated similarity score of these newly introduced weighted rule-based similarity measures among the pairwise rules, and then applied the average linkage clustering using the integrated score. Dynamic tree cut method [,] was then utilized on the resultant dendrogram of the clustering for recognizing co-expressed rule-modules. In addition, we identified the list of evolved condensed markers […]

library_books

A Multiregional Proteomic Survey of the Postnatal Human Brain

2017
Nat Neurosci
PMCID: 5894337
PMID: 29184206
DOI: 10.1038/s41593-017-0011-2

[…] od or brain region, with an additional criteria of a minimum fold change of 2 for genes included in GO analysis.DEX genes over developmental period or brain region were clustered using the R package ‘dynamicTreeCut’. Euclidean distances between genes were clustered using the ‘hclust’ function (method=‘average’) prior to cluster discretisation using a dynamic tree cut (method=‘hybrid’, deepSplit=T, […]

library_books

Comparative transcriptomics reveal developmental turning points during embryogenesis of a hemimetabolous insect, the damselfly Ischnura elegans

2017
Sci Rep
PMCID: 5648782
PMID: 29051502
DOI: 10.1038/s41598-017-13176-8

[…] biological variance between our samples as already indicated by the clustering and MDS analyses (Fig.  and Supplementary Fig. ). However, subsequent quantification of module similarity revealed that DynamicTreeCut might have identified modules which are very similar (Supplementary Fig. ). Therefore modules were merged based on module eigengene correlations of 0.9 (MEDissThres = 0.1). Although mod […]

call_split

Whole transcriptome analysis delineates the human placenta gene network and its associations with fetal growth

2017
BMC Genomics
PMCID: 5502484
PMID: 28693416
DOI: 10.1186/s12864-017-3878-0
call_split See protocol

[…] k. The reciprocal topological dissimilarity matrix was used as input for hierarchical clustering, and gene modules were defined based on hierarchical clustering guided by topological overlap, using a dynamic tree cut algorithm to establish modules []. Finally, highly correlated modules were merged based on a merging threshold set at a height cut-off of 0.25. In the resulting network, as neighbors […]

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Dynamic Tree Cut institution(s)
Department of Human Genetics, University of California at Los Angeles, CA, USA; Rosetta Inpharmatics-Merck Research Laboratories, Seattle, WA, USA
Dynamic Tree Cut funding source(s)
Supported by 1U19AI063603-01 and NINDS/NIMH 1U24NS043562-01.

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