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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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No version available

Documentation


methyAnalysis citations

 (11)
library_books

Zika Virus Alters DNA Methylation of Neural Genes in an Organoid Model of the Developing Human Brain

2018
mSystems
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 […]

library_books

HER2 is not a cancer subtype but rather a pan cancer event and is highly enriched in AR driven breast tumors

2018
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 […]

library_books

Screening of candidate key genes associated with human osteosarcoma using bioinformatics analysis

2017
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 […]

library_books

An integrative analysis of DNA methylation in osteosarcoma

2017
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 […]

library_books

Comprehensive characterization of DNA methylation changes in Fuchs endothelial corneal dystrophy

2017
PLoS One
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 […]

library_books

DNA hypomethylation upregulates expression of the MGAT3 gene in HepG2 cells and leads to changes in N glycosylation of secreted glycoproteins

2016
Sci Rep
PMCID: 4829869
PMID: 27073020
DOI: 10.1038/srep24363

[…] and 10 normal liver samples). differences in the mgat3 promoter methylation were visualized using the r language and environment for statistical computing (r core team, 2015) and the package “methyanalysis”. expression analysis was conducted using the r package “limma”., before collection of glycoproteins, the cells were left to grow in dmem without foetal bovine serum for twenty-four […]


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