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DMAP specifications

Information


Unique identifier OMICS_03430
Name DMAP
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format SAM
Output format Tab-delimited text
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
Computer skills Advanced
Stability Stable
Maintained No

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Publication for DMAP

DMAP in publications

 (8)
PMCID: 5351615
PMID: 28030832
DOI: 10.18632/oncotarget.14042

[…] alignments were performed on a macbook pro with 64 bit duo quad core intel xeon processors and with 22 gb ram running macos 10.6., following alignment, fragment-based methylomes were generated using dmap []. correlation analysis of replicates and initial hierarchical clustering analysis was performed with methylkit []. differential methylation fragment (dmf) analysis of the different groups […]

PMCID: 4938645
PMID: 27172225
DOI: 10.1534/g3.116.030379

[…] indicating effective bisulfite conversion and low levels of true non-cpg methylation., differential methylation analysis was performed using our in-house differential methylation analysis package (dmap) (), which contains two main programs (diffmeth and identgenloc). mspi fragments were used as the unit of analysis for dna methylation. each sample was filtered for fragments that had at least […]

PMCID: 4792177
PMID: 26978482
DOI: 10.1038/sdata.2016.19

[…] after determining the methylation status of the mspi fragments with high coverage, the next step was to annotate these fragments in respect to the genomic features. the identgeneloc program of the dmap package (see code availability 3) was used to associate fragments/ regions with their proximal genes and cpg features. identgeneloc is a command-line program which reads genomic feature table […]

PMCID: 4661471
PMID: 26612583
DOI: 10.1038/srep17328

[…] was performed as our previously published pipelines (details in supplementary methods)., variable methylation analysis was performed with our in-house differential methylation analysis package (dmap). dmap contains two main programs (diffmeth and identgenloc). we used mspi fragments as the unit of analysis for identifying variable methylation. using the diffmeth program, for each individual […]

PMCID: 4537718
PMID: 26301253
DOI: 10.1155/2015/852070

[…] as shown in . from computational perspective, the differential methylation analysis of rna is quite different from that of dna, and dna differential methylation approaches [], such as moabs [] and dmap [], may not be directly applicable to rna. until now, methods aiming at the differential analysis of merip-seq data do not extensively appear in literature. exomepeak [, ] is dedicatedly […]


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DMAP institution(s)
Department of Biochemistry, University of Otago, Dunedin, New Zealand; Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand; Gravida: National Centre for Growth and Development, Auckland, New Zealand

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