methylSig statistics

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Popular tool citations

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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

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Publication for methylSig

methylSig in pipeline

2016
PMCID: 4770084
PMID: 26908133
DOI: 10.1038/ncomms10767

[…] sequencer. 50 bp reads were aligned against a bisulfite-converted human genome (hg19) using bowtie and bismark. downstream analysis was performed using r version 3.0.3, bioconductor 2.13 and the methylsig 0.1.3 package. only genomic regions with coverage between 10 and 500 × were used for the downstream analysis (). dmr were identified by first summarizing the methylation status of genomic […]


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methylSig in publications

 (10)
PMCID: 5617875
PMID: 28955039
DOI: 10.1038/s41598-017-12401-8

[…] 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, […]

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

[…] saap-rrbs [, ]., 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 […]

PMCID: 5369282
PMID: 28377872
DOI: 10.1016/j.molmet.2017.02.001

[…] 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., we queried a mouse liver bayesian network of ∼9400 nodes and ∼18,500 edges generated […]

PMCID: 5138066
PMID: 27980397
DOI: 10.4137/BBI.S38427

[…] 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 […]

PMCID: 5111047
PMID: 27848993
DOI: 10.1038/srep37110

[…] with datasets produced by pooling all considered samples within species. orthologous relationships between genes were then established using orthodb for all genes with 0 or 1 copy in any species., methylsig was used to assess differential methylation between samples. we assessed whether dna methylation differed significantly between castes or sexes using 200 bp windows as established within […]


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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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