methVisual statistics

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Associated diseases

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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

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Publication for methVisual

methVisual in publications

 (3)
PMCID: 5731902
PMID: 29254192
DOI: 10.18632/oncotarget.21356

[…] 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’ []., ovarian cancer cell lines (a2780, a2780cis and skov3) were seeded in 35 mm dishes at a density of 1×105 cells/dish 1 day before drug treatment. cells were treated with 10 μm 5-aza-dc […]

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

[…] 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 […]

PMCID: 3777004
PMID: 23982603
DOI: 10.1038/bjc.2013.496

[…] 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 […]


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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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