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Protocols

methylSig specifications

Information


Unique identifier OMICS_04054
Name methylSig
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Publication for methylSig

methylSig citations

 (15)
library_books

msgbsR: An R package for analysing methylation sensitive restriction enzyme sequencing data

2018
Sci Rep
PMCID: 5794748
PMID: 29391490
DOI: 10.1038/s41598-018-19655-w

[…] knowledge users may wish to use other bioinformatics tools to perform differential methylation analyses. Users may want to perform other normalisation methods or use other downstream packages such as methylSig, BiSeq or DSS, packages designed to identify differentially methylated sites and regions. However, these tools have been primarily designed to work with whole genome bisulphite (WGBS) sequen […]

library_books

Similarity Based Segmentation of Multi Dimensional Signals

2017
Sci Rep
PMCID: 5617875
PMID: 28955039
DOI: 10.1038/s41598-017-12401-8

[…] ferentially methylated regions (DMRs) from whole genome bisulfite sequencing data. While some tools use simple heuristics to aggregate differentially methylated CpGs into DMRs (e.g. BS-seq, MOABS, or MethylSig). More recently, HMM based methods such as HMM-Fisher have been introduced.Another important variation on the theme are reference-based transcriptome assemblers such as cufflinks, TruHMM, OR […]

library_books

Alterations of sorbin and SH3 domain containing 3 (SORBS3) in human skeletal muscle following Roux en Y gastric bypass surgery

2017
Clin Epigenetics
PMCID: 5581422
PMID: 28883895
DOI: 10.1186/s13148-017-0396-5

[…] Differences in methylation sites were assessed in participants pre- and post-surgery. The aligned (Hg19) sequencing data was imported into the free open source R package, methylSig []. A minimum of five reads and the recovery of the site in all seven participants from pre- and post-surgery were required for the inclusion of a cytosine in subsequent analyses. The mean m […]

call_split

DNA methylation alters transcriptional rates of differentially expressed genes and contributes to pathophysiology in mice fed a high fat diet

2017
PMCID: 5369282
PMID: 28377872
DOI: 10.1016/j.molmet.2017.02.001
call_split See protocol

[…] es were sequenced on a Hiseq2000 (Illumina) using 100 bp paired end reads. Quality and adaptor trimming were done using Trim Galore and alignment was performed using Bismark. Duplicates were removed. MethylSig was used for differential methylation analysis , . The GEO accession number for this study is GSE85425. […]

library_books

TEA: the epigenome platform for Arabidopsis methylome study

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

[…] thylation 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 defining differentially methylated genes (DMGs) as genes […]

library_books

Integrating Epigenomics into the Understanding of Biomedical Insight

2016
Bioinform Biol Insights
PMCID: 5138066
PMID: 27980397
DOI: 10.4137/BBI.S38427

[…] linear model (BSmooth), bump hunting with batch effect removal and peak detection (bumphunting), tunable kernel smoothing (DMR-cate), nonparametric and kernel-based method (M3D), beta-binomial model (methylSig), beta-binomial hierarchical model (MOABS), hidden Markov model (NHMMfdr), three-state HMM (MethPipe), Shannon entropy (QDMR), and a binary segmentation algorithm combined with a two-dimensi […]

Citations

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methylSig institution(s)
Department of Computational Medicine and Bioinformatics, Pathology Department, Department of Environmental Health Sciences, Department of Otolaryngology and Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA

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