MethylAction specifications

Information


Unique identifier OMICS_10958
Name MethylAction
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Read alignments
Output data Differentially methylated regions
Operating system Unix/Linux, Mac OS
Programming languages R
License MIT License
Computer skills Advanced
Version 2.0
Stability Stable
Requirements
Data.table, GenomicRanges, IRanges, DESeq, goldmine
Maintained Yes

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Documentation


Maintainer


  • person_outline Jeffrey Bhasin <>

Publication for MethylAction

MethylAction in publication

PMCID: 4937336
PMID: 27257071
DOI: 10.1093/nar/gkw477

[…] nearly twice as large as the other two donors, and these samples were downsampled to match the mean of the depth (57 349 008 reads) from the other samples using samtools., dmrs were detected using methylaction (). a window size of 50 bp and a fragment size of 266 bp were selected based on the protocol referenced in the geo records. a subject-level effect was added to the testing model […]


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MethylAction institution(s)
Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
MethylAction funding source(s)
National Cancer Institute of the National Institutes of Health [R01CA154356, F31CA195887]

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