ENmix protocols

View ENmix computational protocol

ENmix statistics

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chevron_left oxBS/TAB/fCAB/CAB-seq Methylation scoring Hydroxymethylation analysis Background correction chevron_right
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ENmix specifications

Information


Unique identifier OMICS_09981
Name ENmix
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.16.0
Stability Stable
Requirements
stats, parallel, graphics, BiocGenerics, grDevices, RUnit, preprocessCore, MASS, foreach, SummarizedExperiment(>=1.1.6), geneplotter, doParallel, sva, minfi(>=1.22.0), RPMM, impute, wateRmelon, minfiData(>=0.4.1)
Maintained Yes

Subtool


  • oxBS-MLE

Versioning


Add your version

Documentation


Maintainer


  • person_outline Zongli Xu <>

Publications for ENmix

ENmix in pipelines

 (2)
2018
PMCID: 5907140
PMID: 29671397
DOI: 10.1186/s12859-018-2096-3

[…] infinium i/ii bias. r package missmethyl is suitable for go term enrichment analysis and biological interpretation. in our view, minfi is a proper r package to import data, eliminate background and enmix package can be used to correct the type bias, then the normalized data should be used in the remaining steps of the framework., none declared., publication costs were funded by the major state […]

2017
PMCID: 5428306
PMID: 28325913
DOI: 10.1038/s41598-017-00384-5

[…] across all cord blood samples and used univariate linear regression models to explore associations among each of the top 30-principal components with phenotypic and technical covariates using the enmix bioconductor package of r. all analyses were carried out using the r statistical package, version 3.2.3 (www.r-project.org/)., we examined the association of prenatal mercury exposure […]


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ENmix in publications

 (3)
PMCID: 5943364
PMID: 29743579
DOI: 10.1038/s41598-018-24240-2

[…] was performed using the ssnoob method. probes from the x and y chromosome were removed to exclude sex variability and probe type bias was corrected using the rcp method as described in the enmix bioconductor package (1.12.0). individual beta values for each sample were calculated for further statistical analysis. beta values are defined as the ratio of methylated probe intensity […]

PMCID: 5922319
PMID: 29695247
DOI: 10.1186/s12864-018-4652-7

[…] beadchip., quality control (qc) and all statistical analyses were performed using the r version 3.2.5 statistical analysis software [], and the r-packages minfi [], watermelon [], enmix [], sva [], limma [], and mediation []., methylation intensity signals were extracted from raw intensity data using the preprocessenmix procedure []. this includes background noise correction […]

PMCID: 5907140
PMID: 29671397
DOI: 10.1186/s12859-018-2096-3

[…] infinium i/ii bias. r package missmethyl is suitable for go term enrichment analysis and biological interpretation. in our view, minfi is a proper r package to import data, eliminate background and enmix package can be used to correct the type bias, then the normalized data should be used in the remaining steps of the framework., none declared., publication costs were funded by the major state […]


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ENmix institution(s)
Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA; Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA; Department of Environmental Health, College of Medicine, University of Cincinnati, Cincinnati, OH, USA; Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
ENmix funding source(s)
Intramural Research Program of the NIH, National Institute of Environmental Health Sciences [Z01 ES044005, Z01 ES101765, Z01 ES049033, Z01 ES049032]

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