ConsensusClusterPlus statistics

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ConsensusClusterPlus specifications

Information


Unique identifier OMICS_14380
Name ConsensusClusterPlus
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A data matrix and user-specified options.
Output data An R data objectis, a text file, a graphical plot or a log file.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.44.0
Stability Stable
Requirements
stats, graphics, Biobase, utils, cluster, ALL
Maintained Yes

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Maintainer


  • person_outline Matthew Wilkerson <>

Publication for ConsensusClusterPlus

ConsensusClusterPlus in publications

 (72)
PMCID: 5958058
PMID: 29773832
DOI: 10.1038/s41467-018-04383-6

[…] 23 samples). for histone marks, chip-seq data were filtered as follows: − log10(fdr) > 10 and number of samples that share the peak > 3. for sequence or chip-based data, an extension of the consensusclusterplus algorithm was used. in brief, using all paired combination of pearson’s distance and different linkage metrics (ward, complete and average), hierarchical clustering […]

PMCID: 5895731
PMID: 29675033
DOI: 10.3389/fgene.2018.00108

[…] as performance evaluation metric ()., for every testing data set, between 35 and 50 genes were chosen in the feature selection, which combined to a total of 81 unique classifier genes., we used the consensusclusterplus package () with ward’s clustering and spearman correlation distance metric to cluster genes in m1–m6. the optimal number of clusters k = 4 was obtained by investigating […]

PMCID: 5882098
PMID: 29614076
DOI: 10.1371/journal.pone.0192726

[…] to the best human performance value for each evaluation metric. a two-sample kolmogorov-smirnov test was used to compare two distributions. unsupervised clustering was performed using the package consensusclusterplus in r []., the authors acknowledge nvidia corporation for the gift of a titan-x gpu. j.j.n. would like to thank dr. erika holzbaur for the opportunity and the support to pursue […]

PMCID: 5849599
PMID: 29535388
DOI: 10.1038/s41467-018-03099-x

[…] prior to any clustering analysis did not detect any evidence of batch effects., after median centering the log2(rsem + 1) values by gene, unsupervised consensus clustering was applied using the consensusclusterplus r package, with partitioning around medioids and a spearman correlation-based distance. additional hierarchical clustering of the consensus clustering classes was performed, […]

PMCID: 5843664
PMID: 29520031
DOI: 10.1038/s41467-018-03121-2

[…] where ∩ denotes intersection between altered proteomes i and j, and ⋃ denotes union between altered proteomes iand j., consensus clustering was performed using the r package consensusclusterplus. samples were clustered using euclidean distance as the distance measure. a total of 2538 proteins in d6 were used for k-means clustering with up to 6 clusters. the consensus […]


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ConsensusClusterPlus institution(s)
Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Internal Medicine, Division of Medical Oncology, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
ConsensusClusterPlus funding source(s)
This work was supported by National Cancer Institute (NCI) F32CA142039, Thomas G. Labrecque Foundation through Joan’s Legacy Foundation, and National Institutes of Health (NIH) U24CA126554.

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