methylKit specifications


Unique identifier OMICS_00606
Name methylKit
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format Tab-delimited text
Output format Bedgraph, tab-delimited text, images
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Christopher E. Mason <>

methylKit article

methylKit citations

PMCID: 5905506

[…] level of each sampled cytosine was estimated as the number of reads reporting a c, divided by the total number of reads reporting a c or t., differentially methylated cpg regions were analysed using methylkit [33]. sex of the fish was used as a co-variate in the analysis. briefly, the numbers of methylated and unmethylated cpg sites were counted for each region and descriptive statistics […]

PMCID: 5627257

[…] (compared to the 5507 cpgs identified as asm sites in the permutated datasets). to minimize false positives, the identified asm candidate sites were clustered into regions as previously described36. methylkit r package51 was used to perform the hierarchical clustering of the methylation profiles. the dmrs between each los fetus and all four controls were identified using the bsseq r package30., […]

PMCID: 4790440

[…] of regression beta coefficients, dmr identification above lower threshold and permutation for dmr confidence assessment. the method customized for 450k array is part of r minfi package [23]. methylkit uses a sliding window approach or intersects with predefined genomic regions such as cpg island, promoter, etc. to aggregate methylated and unmethylated c counts and then conduct […]

PMCID: 4405367

[…] for sperm, we performed rrbs in triplicates on sperm pooled from three exposed animals, as well as five control pools from unexposed animals. to find differences in dna methylation, we used the methylkit r package to search for changes in methylation greater than 20% in 400bp tiles containing at least 3 cpgs. all data processing and representation were performed with the r software […]

methylKit institution(s)
Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY USA; Department of Public Health, Weill Cornell Medical College, New York, NY, USA; Department of Medicine, Division of Hematology/Oncology, Weill Cornell Medical College, New York, NY, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Pharmacology, Weill Cornell Medical College, New York, NY, USA

methylKit review

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