MethylAction specifications


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
Data.table, GenomicRanges, IRanges, DESeq, goldmine
Maintained Yes


No version available



  • person_outline Jeffrey Bhasin

Publication for MethylAction

MethylAction citations


Interplay between maternal Slc6a4 mutation and prenatal stress: a possible mechanism for autistic behavior development

Sci Rep
PMCID: 5562880
PMID: 28821725
DOI: 10.1038/s41598-017-07405-3

[…] DNA methylation was assessed using R-based pipelines MEDIPS and MethylAction with parameters described in the Supplementary Information. Differentially methylated regions (DMRs) called by both pipelines were used in the downstream analysis. One sample with low enr […]


Goldmine integrates information placing genomic ranges into meaningful biological contexts

Nucleic Acids Res
PMCID: 4937336
PMID: 27257071
DOI: 10.1093/nar/gkw477

[…] The drawGenomePool() option was used to draw a length-matched genomic null set of regions to the DMRs, sampling 100 times more regions than the query. These ranges were concatenated with the filtered MethylAction DMR set. The goldmine() function was run using these gene and feature lists and the GenomicRanges object containing both the DMRs and null regions as the query ranges. Resulting annotated […]

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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