methylMnM statistics

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methylMnM specifications

Information


Unique identifier OMICS_02047
Name methylMnM
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 1.18.0
Stability Stable
Requirements
edgeR, statmod, R(>=2.12.1)
Maintained Yes

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Documentation


methylMnM in publications

 (5)
PMCID: 5813940
PMID: 29447215
DOI: 10.1371/journal.pone.0192606

[…] a log fold change (logfc) with an absolute value greater than 2 was considered differentially expressed. for the methylation analysis, we combined the mre-seq and medip-seq data using the r package methylmnm [] to find differentially methylated regions (dmrs) due to maternal diet. since setting a significance threshold is somewhat arbitrary, we determined how many windows had a q-value […]

PMCID: 5237802
PMID: 28088687
DOI: 10.1016/j.neo.2016.12.009

[…] and scoring consisted of tabulating reads with cpgs at each fragment end. all data methylation values were predicted by methylcrf based on medip and mre signals according to published methods ., the methylmnm package (http://epigenome.wustl.edu/mnm/) was used to identify dmrs in the r 2.0.15 environment. default parameters were used, and a statistical cutoff of q value <10−9 was applied […]

PMCID: 4829722
PMID: 27123440
DOI: 10.1155/2016/4395153

[…] using bwa-mem li [] with default settings., we used an algorithm named m&m [] that integrates data from both medip-seq and mre-seq to detect dmrs. m&m is available as an r package called “methylmnm.” briefly, m&m integrates medip-seq and mre-seq by dynamically scaling, normalizing, and combining the datasets and provides exact p value and q-value for different sample comparison. […]

PMCID: 4339225
PMID: 25697895
DOI: 10.1038/ncomms7315

[…] the manufacturer’s instructions. the data were analyzed with the pyromark q24 software (qiagen)., differentially methylated regions (dmrs) between developmental stages were identified by using methylmnm package, with the default parameters in r environment. briefly, the coverage of medip and mre sequencing data and genomic cpg information were calculated in each 500-bp genomic bin. […]

PMCID: 4198682
PMID: 25286960
DOI: 10.1186/1471-2164-15-868

[…] mrna expression levels of target genes were quantified using the 2-δδct equation for endometrial normal and cancer tissues. mean ct of normal endometrium was used as the calibrator sample., the methylmnm package (http://epigenome.wustl.edu/mnm/) was utilized to identify differentially methylated regions (dmrs) in the r 2.15 environment between the dna methylome of normal endometrium […]


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