swDMR statistics

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Citations per year

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Popular tool citations

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swDMR specifications

Information


Unique identifier OMICS_00625
Name swDMR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl, R
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


swDMR in pipeline

2015
PMCID: 4606454
PMID: 26344546
DOI: 10.7554/eLife.06671.030

[…] tair10) using bismark v0.14.3 () with default parameters; the pcr duplicates were removed, and the methylation information was obtained with bismark with cutoff 3. the dmrs were obtained using swdmr () with window 200, step size 100, (left 1000, right 1000), the samples were compared using the kruskal–wallis analysis of variance with p-value < 0.01. the dmrs were then annotated using […]


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swDMR in publications

 (10)
PMCID: 5717273
PMID: 29208987
DOI: 10.1038/s41598-017-17046-1

[…] the distributions of methylation level were irregular in both trained and untrained groups.figure 3 , differentially methylated regions between the trained and untrained groups were identified using swdmr software with rigorous parameters. a total of 853 dmrs throughout the whole genome were identified (table ). in order to explore the relationship between dna methylation and gene transcription, […]

PMCID: 5787839
PMID: 28796917
DOI: 10.1111/pbi.12820

[…] proportion of mcs in three contexts was calculated as the proportion of mcg, mchg and mchh on the total mc sites, respectively (figure a). differentially methylated regions (dmrs) were identified by swdmr software (http://122.228.158.106/swdmr/), which applied a sliding‐window approach. the window was 1000 bp and step length was 100 bp. the fisher test was applied to detect significant dmrs. […]

PMCID: 5557475
PMID: 28806912
DOI: 10.1186/s12864-017-3962-5

[…] icipate in regulating the dmgs to influence biological processes. by a genome-wide comparison of dna methylation sequences between njcms5a and njcms5b, 3527 dmrs (additional file ) were identified by swdmr software (https://sourceforge.net/projects/swdmr/) with “fdr ≤ 0.05 and coverage changes ≥ 5” in this study. then, dmgs were defined as genes overlapping with significant dmrs with at least 1 bp […]

PMCID: 5542662
PMID: 28771560
DOI: 10.1371/journal.pone.0182492

[…] between japanese black cattle (wagyu) and chinese red steppes, we referenced the modeled of hao. y. et al [] to estimate methylation level []. dmrs were identified using a sliding-window approach of swdmr software (http://122.228.158.106/swdmr/) [] and the window is set to 1000 bp and step length at 100 bp. fisher test is implemented to detect the dmrs., gene related to dmrs were implemented […]

PMCID: 5390369
PMID: 28407801
DOI: 10.1186/s12864-017-3681-y

[…] \setlength{\oddsidemargin}{-69pt} \begin{document}$$ ml\ (corrected) = \frac{ml- r}{1- r} $$\end{document}mlcorrected=ml−r1−r , differentially methylated regions (dmrs) were identified using the swdmr software (http://122.228.158.106/swdmr/), which uses a sliding-window approach. the window is setto 1000 bp and step length is 100 bp. fisher test is implemented to detect the dmrs., gene ontolo […]


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