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clusterStab specifications

Information


Unique identifier OMICS_20499
Name clusterStab
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.52.0
Stability Stable
Requirements
methods, genefilter, R(>=1.9.0), fibroEset, Biobase(>=1.4.22)
Maintained Yes

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Maintainer


  • person_outline James MacDonald <>

clusterStab in publications

 (5)
PMCID: 5780444
PMID: 29403457
DOI: 10.3389/fmicb.2018.00002

[…] was performed with varying numbers of clusters (k = 2–7), and the distribution of the jaccard coefficients obtained was displayed as a histogram. the benhur function in the r/bioconductor package “clusterstab” was used to carry out the clustering and calculation. the dendrogram of ma-lmm01 expression clusters was plotted using the dendrogram function (hclust; r package stats). the heat map […]

PMCID: 5335546
PMID: 27187794
DOI: 10.1038/ismej.2016.81

[…] to determine the number of stable clusters as described previously (). briefly, the scaled log2rpkm data set was hierarchically clustered using pearson's correlation and resampled using the clusterstab r package ()., host genes found de between infected and control samples at every time point (see above) were placed into one of 14 functional categories based on mg-rast () (i.e., […]

PMCID: 2891634
PMID: 20492709
DOI: 10.1186/1471-2407-10-222

[…] 16 ovarian samples with ambiguous diagnosis were introduced in the dataset and the clustering was performed., validation of the reference hierarchical tree was performed using r environment and the clusterstab package []. this package assessed the number of reliable clusters and the stability of the hierarchical clustering with a re-sampling approach whereby randomly selected subsets of samples […]

PMCID: 2762038
PMID: 19847310
DOI: 10.1371/journal.pone.0007556

[…] are generally used without any assessment of the statistical robustness of the identified clusters . in the present study we use the resampling-based method implemented in the bioconductor package “clusterstab” to determine both the optimal number of clusters and the statistical significance of the final clustering . the differential gene expression between the significant clusters […]

PMCID: 2676303
PMID: 19348669
DOI: 10.1186/1471-2164-10-147

[…] fe deficiency were subjected to a cluster analysis using k-means methods with the algorithm as described previously []. the cluster stability was determined using the "benhur" function found in the clusterstab package of the bioconductor software . apart from a two-cluster model that was not useful in analyzing the response to fe deficiency, a six-cluster model generated the smallest number […]


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