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LumiWCluster specifications

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Unique identifier OMICS_18710
Name LumiWCluster
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 1.0
Stability Beta
Source code URL http://www.ams.sunysb.edu/~pfkuan/LumiWCluster/LumiWCluster_1.0.tar.gz
Maintained Yes

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Maintainer


  • person_outline Pei Fen Kuan <>

Publication for LumiWCluster

LumiWCluster in publications

 (3)
PMCID: 3777004
PMID: 23982603
DOI: 10.1038/bjc.2013.496

[…] with missing values, those residing on the x chromosome, and those with a median detection p-value >0.05 across samples can be filtered out; other packages allowing such filtering include (; )., lumiwcluster () includes a function for model-based clustering of methylation data using a weighted likelihood approach wherein higher-quality samples (i.e., those with a low median detection […]

PMCID: 3554647
PMID: 23358896
DOI: 10.1371/journal.pone.0054742

[…] in hpv(+) and hpv(−) tumors. the effects of clinical characteristics on dna cpg methylation measured on the goldengate array were examined using limma in r 2.10.1 . sample weights generated with lumiwcluster based on detection p-values across samples were used in the lmfit function from the limma package to downweight samples with higher detection p-values. cpg sites were identified […]

PMCID: 3566828
PMID: 23287992
DOI: 10.1038/bjc.2012.568

[…] island methylator phenotype (cimp) were validated using rand index., methylation data from tumour samples were normalised for sequence length and gc content, and important probes were selected using lumiwcluster package, thus eliminating arbitrary detection p-value cutoffs in removing unreliable methylation values (). wilcoxon rank sum test was employed in identifying statistically significant […]

LumiWCluster institution(s)
Department of Biostatistics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA; Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA
LumiWCluster funding source(s)
Supported by NCI (grants 5-P30-CA16086-34 and 1R21CA134368- 01A1); Susan G. Komen Foundation (grant KG081397).

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