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Protocols

methVisual specifications

Information


Unique identifier OMICS_00604
Name methVisual
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.32.0
Stability Stable
Requirements
stats, grid, graphics, IRanges, utils, Biostrings, grDevices, R(>=2.11.0), Biostrings(>=2.4.8), plotrix, gsubfn, sqldf, ca, gridBase
Maintained Yes

Versioning


No version available

Documentation


Publication for methVisual

methVisual citations

 (4)
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Inhibition of coiled coil domain containing protein 69 enhances platinum induced apoptosis in ovarian cancer cells

2017
Oncotarget
PMCID: 5731902
PMID: 29254192
DOI: 10.18632/oncotarget.21356
call_split See protocol

[…] ld a 640 bp product. PCR products were cloned into TOPO® TA cloning Vector [Invitrogen]), and 10 white colonies were randomly chosen for sequencing. DNA methylation data were visualized by R package ‘methVisual’ []. […]

library_books

CpG location and methylation level are crucial factors for the early detection of oral squamous cell carcinoma in brushing samples using bisulfite sequencing of a 13 gene panel

2017
Clin Epigenetics
PMCID: 5558660
PMID: 28814981
DOI: 10.1186/s13148-017-0386-7

[…] are user friendly. Using perl to recognize specific sequence motifs, several FASTA files were created for each gene for each patient and then loaded onto a visualization tool such as BiQ Analyzer [], MethVisual [], QUMA [], or BISMA []. However, these tools do not scale up with massively parallel sequencing having been designed for Sanger sequencing. Newer tools such as Bismark [] and BS-Seeker [] […]

library_books

Small Magnitude Effect Sizes in Epigenetic End Points are Important in Children’s Environmental Health Studies: The Children’s Environmental Health and Disease Prevention Research Center’s Epigenetics Working Group

2017
Environ Health Perspect
PMCID: 5382002
PMID: 28362264
DOI: 10.1289/EHP595

[…] n to compare methylation values across samples, tissues, or other categories. Approaches implemented depend on the type of data analyzed.R packages that can implement some of all of the above include MethVisual (), methyAnalysis (version 1.12.0; R Project for Statistical Computing), Methylation plotter (), MethTools (), MethylMix (), IMA (), coMET (), and minfi () (). Most of these enable implemen […]

library_books

Review of processing and analysis methods for DNA methylation array data

2013
Br J Cancer
PMCID: 3777004
PMID: 23982603
DOI: 10.1038/bjc.2013.496

[…] then that locus is considered to be differentially methylated. This 0.2 threshold corresponds to the recommended difference in methylation between samples that can be detected with 99% confidence (). MethVisual () tests whether each CpG site has independent membership between two groups using Fisher's exact test; other packages include (; ; ; ), some allowing for the adjustment of potential confou […]

Citations

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methVisual institution(s)
Department of Computational Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany; Department Microbiology and Molecular Genetics, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel
methVisual funding source(s)
EU IP grant EUTRACC and FastTrack (Robert Bosch Foundation), a grant of the Friedrich Ebert Foundation

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