methyAnalysis protocols

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chevron_left Differentially methylated region detection Data visualization chevron_right
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methyAnalysis specifications

Information


Unique identifier OMICS_02046
Name methyAnalysis
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 1.22.0
Stability Stable
Requirements
AnnotationDbi, methods, stats, parallel, grid, BiocGenerics, IRanges, GenomicRanges, utils, GenomeInfoDb, rtracklayer, grDevices, SummarizedExperiment, Gviz, R(>=2.10), biomaRt, GenomicFeatures, genefilter, Biobase(>=2.5.5), org.Hs.eg.db, annotate, VariantAnnotation, lumi, methylumi, Biobase(>=2.34.0), genoset
Maintained Yes

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Documentation


methyAnalysis in pipelines

 (2)
2014
PMCID: 4070873
PMID: 24898317
DOI: 10.1186/1471-2164-15-435

[…] context of dmps we used hm450 annotations, with hg19 as the human reference genome. other genomic features were obtained from a recent publication using hm450 bead arrays []. finally, we used the “methyanalysis” package to identify differentially methylated regions (dmrs) after transforming our dataset to a list of genomic regions followed by methylation data smoothing, as described (pan du […]

2014
PMCID: 4203020
PMID: 25247593
DOI: 10.1038/tp.2014.94

[…] from the pairs of values for all categorical variables and examined for differential methylation using (a) linear modelling using limma, including adjustment for multiple testing and (b) the methyanalysis package to smooth processed data and identify differentially methylated regions by use of t-tests applied between groups (also bh-corrected for multiple testing)., gene set enrichment […]


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methyAnalysis in publications

 (10)
PMCID: 5801341
PMID: 29435496
DOI: 10.1128/mSystems.00219-17

[…] was performed with the r q value package. for the 1-kb tiles, at least 5 cpgs were required to be covered at 5×. for the 100-bp tiles, at least 2 cpgs were required to be covered at 5×. the r methyanalysis with the txdb.hsapiens.ucsc.hg19.knowngene package was used to associate genes with dmrs. the r dose () package was used for disease ontology analyses. a background gene list […]

PMCID: 5791377
PMID: 29382369
DOI: 10.1186/s13058-018-0933-y

[…] beadchip methylation data are from nci's genomic data commons (https://gdc.cancer.gov). data were processed with an internal pipeline based on r/bioconductor packages methylumi and methyanalysis, for quality and color balance assessment, color balance adjustment, background adjustment, normalization and methylation modeling. we used the lumi bioconductor package […]

PMCID: 5588164
PMID: 28928828
DOI: 10.3892/ol.2017.6519

[…] 19 os cell lines and 6 normal controls. differentially expressed genes (degs) in the os cell lines were identified using the limma package, and differentially methylated regions were screened with methyanalysis in r. copy number analysis was performed and genes with copy number gains/losses were further screened using dnacopy and cghmcr packages. functional enrichment analyses were performed […]

PMCID: 5715438
PMID: 29234590
DOI: 10.1016/j.jbo.2017.05.001

[…] , in bioconductor . subsequently, the differentially methylated regions (dmr) between osteosarcoma and normal samples were identified using methyanalysis with m-value>1 and false discovery rate (fdr)<0.01., m-values were calculated by the formula:(1)m−value=log2methylated probe intensityunmethylated probe intensity, fdr method […]

PMCID: 5383226
PMID: 28384203
DOI: 10.1371/journal.pone.0175112

[…] using methylumi anon. bioconductor—methylumi. available at: http://www.bioconductor.org/packages/release/bioc/html/methylumi.html [accessed june 18, 2015] and methanalysis anon. bioconductor—methyanalysis. available at: http://www.bioconductor.org/packages/release/bioc/html/methyanalysis.html [accessed june 18, 2015] packages. after excluding probes mapping to genomic regions containing […]


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