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Protocols

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

Versioning


No version available

Documentation


swDMR citations

 (12)
library_books

Genome wide DNA methylation changes associated with olfactory learning and memory in Apis mellifera

2017
Sci Rep
PMCID: 5717273
PMID: 29208987
DOI: 10.1038/s41598-017-17046-1

[…] Differentially methylated regions (DMRs) were identified based on the methylation imformation of each site using the swDMR software developed by Wang et al. and the corresponding procedures. At first, a sliding-window approach with window size of 1000 bp and step length of 100 bp were adopted to scan the genome of t […]

library_books

Single‐base methylome analysis reveals dynamic epigenomic differences associated with water deficit in apple

2017
Plant Biotechnol J
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. Afte […]

library_books

Genome wide comparative analysis of DNA methylation between soybean cytoplasmic male sterile line NJCMS5A and its maintainer NJCMS5B

2017
BMC Genomics
PMCID: 5557475
PMID: 28806912
DOI: 10.1186/s12864-017-3962-5

[…] ional region (promoter, 5′UTR, exon, intron, and 3′UTR) under three different contexts (CG, CHG and CHH).Differentially methylated regions (DMRs) between NJCMS5A and NJCMS5B were identified using the swDMR software (https://sourceforge.net/projects/swdmr/) with a sliding-window approach []. The window is set to 1000 bp and step length is 100 bp. Fisher test is used to detect the DMRs with “FDR ≤ 0 […]

library_books

Comparative genome wide methylation analysis of longissimus dorsi muscles between Japanese black (Wagyu) and Chinese Red Steppes cattle

2017
PLoS One
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. […]

library_books

Single base resolution methylomes of upland cotton (Gossypium hirsutum L.) reveal epigenome modifications in response to drought stress

2017
BMC Genomics
PMCID: 5390369
PMID: 28407801
DOI: 10.1186/s12864-017-3681-y

[…] 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. […]

call_split

Genome wide DNA methylation profiles reveal novel candidate genes associated with meat quality at different age stages in hens

2017
Sci Rep
PMCID: 5381223
PMID: 28378745
DOI: 10.1038/srep45564
call_split See protocol

[…] To determine the differential methylation regions between the two age groups, the present study used swDMR software (http://122.228.158.106/swDMR/), and a sliding-window approach (Select every 1000 bp as a window, with 100 bp as the step length) was performed to identify the differential methylation […]

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