SwDMR
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Application data |
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| Created by | Xianfeng Li |
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| Biological application domain(s) | Bisulfite Sequencing, Differential methylated regions identification |
| Principal bioinformatics method(s) | Differentially methylated regions identification and annotation |
| Technology | Any |
| Created at | Institute of Genomic Medicine, Wenzhou Medical College, Wenzhou 325035, China |
| Maintained? | Yes |
| Input format(s) | Others |
| Output format(s) | Regions, Wiggle, PDF, SVG |
| Software features | Differentially methylated regions identification and annotation |
| Programming language(s) | Perl, R |
| Licence | GPL v3 |
| Operating system(s) | Linux, UNIX |
Summary: swDMR: a sliding window approach to identify differentially methylated regions based on bisulfite sequencing
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Contents
Description
swDMR is a sliding window approach, which is used to identify differentially methylated regions (DMRs) from bisulfite sequencing dataset at single base resolution. The dataset, like whole genome bisulfite sequencing (WGBS) or reduced representation bisulfite sequencing (RRBS) with the same coverage region of samples, are suitable for swDMR.
This software integrated several useful statistics methods, satisfying to two or multiple samples test. It is flexible to identify DMRs from samples with several options. In addition, swDMR provides genomic features annotation with BED or GFF file. It can also produce WIG format file to upload to UCSC genome browser for DMRs visualization.
To successfully run this software, Perl v5.8.8 or later and R 2.12.0 or later are recommended.
Change log
swDMR-1.0.0
Tue Sep 11 15:07:34 CST 2012: Renew the statistics.pm file
Links
References
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