DMAP statistics

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Citations per year

Number of citations per year for the bioinformatics software tool DMAP
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Tool usage distribution map

This map represents all the scientific publications referring to DMAP per scientific context
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Associated diseases

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Popular tool citations

chevron_left Differentially methylated region detection Methylation scoring Methylation annotation chevron_right
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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 Yes

Versioning


No version available

Maintainer


  • person_outline Peter A. Stockwell

Publication for DMAP

DMAP citations

 (7)
library_books

TEA: the epigenome platform for Arabidopsis methylome study

2016
BMC Genomics
PMCID: 5260138
PMID: 28155665
DOI: 10.1186/s12864-016-3326-6

[…] eads mapped to the position to give the cytosine methylation measurement at each C in the genome. Tools have been developed to deal with whole-genome BS-Seq (WGBS) data, such as BiSeq [], BSmooth [], DMAP [], methPipe [], methylKit [], methylPipe [], methylSig [], MOABS [], radMeth [], and WBSA []. Most of these analysis tools focus on identifying differentially methylated regions (DMRs) and defin […]

library_books

Genome wide methylation sequencing of paired primary and metastatic cell lines identifies common DNA methylation changes and a role for EBF3 as a candidate epigenetic driver of melanoma metastasis

2016
Oncotarget
PMCID: 5351615
PMID: 28030832
DOI: 10.18632/oncotarget.14042

[…] 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 was p […]

library_books

Placental Hypomethylation Is More Pronounced in Genomic Loci Devoid of Retroelements

2016
PMCID: 4938645
PMID: 27172225
DOI: 10.1534/g3.116.030379

[…] nt), 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 tw […]

library_books

Genome scale DNA methylome and transcriptome profiling of human neutrophils

2016
Sci Data
PMCID: 4792177
PMID: 26978482
DOI: 10.1038/sdata.2016.19

[…] t of analysis. We selected the fragments having 10 or more reads at≥2 CpG sites in each individual to provide fragment-based methylomes for these individuals (F2 t10 switch in the diffmeth program of DMAP tool, see Code availability 3). Data Citation 1 contains these fragment-based methylomes for the 13 RRBS libraries described in this article. […]

library_books

Detection of differentially methylated regions from whole genome bisulfite sequencing data without replicates

2015
Nucleic Acids Res
PMCID: 4666378
PMID: 26184873
DOI: 10.1093/nar/gkv715

[…] on levels between biological conditions. A number of statistical methods and computational tools have been developed recently, including BSmooth (), MethylKit (), GBSA (), BiSeq (), DSS (), MOABS (), DMAP (), MethylSig () and Bisulfighter ().Similar to other sequencing experiments, the raw data from WGBS experiments are short sequence reads. After alignment and data processing, the data can be sum […]

library_books

Base resolution DNA methylation landscape of zebrafish brain and liver

2014
Genom Data
PMCID: 4535936
PMID: 26484126
DOI: 10.1016/j.gdata.2014.10.008

[…] the end of sequenced reads, therefore the reads were hard-trimmed from 100 bp to 65 bp to improve data quality. The adaptor sequences from the reads were removed with the cleanadaptors program of the DMAP package as previously described , . The brain methylome dataset (read length = 49 bp) contained negligible levels of adaptor sequences (evaluated with cleanadaptors and FastQC). […]


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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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