methylKit protocols

methylKit specifications

Information


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

Versioning


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Documentation


Maintainer


  • person_outline Christopher E. Mason <>

Publication for methylKit

methylKit IN pipelines

 (9)
2018
PMCID: 5905506
PMID: 29686887
DOI: 10.1093/eep/dvy005

[…] 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 […]

2017
PMCID: 5389146
PMID: 28413451
DOI: 10.1186/s13072-017-0126-4

[…] bioinformatics), followed by bismark alignment (version 0.14.5, babraham bioinformatics, [30]) to the recently released zebrafish genome assembly grcz10. downstream analysis was performed with the methylkit package in r (version 3.2.2), using logistic regression analysis with a sliding linear model to correct for multiple comparisons, using benjamini–hochberg false discovery rate (fdr) […]

2017
PMCID: 5389146
PMID: 28413451
DOI: 10.1186/s13072-017-0126-4

[…] 3.2.2), using logistic regression analysis with a sliding linear model to correct for multiple comparisons, using benjamini–hochberg false discovery rate (fdr) correction (q-value) [60]. within methylkit, our approach was to detect differentially methylated regions (dmrs) by dividing the genome in 300-bp tiles containing at least 4 mutually covered cs in cpg context, with at least 5 reads […]

2017
PMCID: 5627257
PMID: 28978943
DOI: 10.1038/s41598-017-13012-z

[…] (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., […]

2017
PMCID: 5634322
PMID: 28994822
DOI: 10.1038/sdata.2017.148

[…] integrative genome view14. subsequent differential methylation analysis using these data can be carried out using the r/bioconductor package bsseq11,15 or other publicly available packages such as methylkit16 may also be used for this analysis., our data set will be useful for a variety of studies investigating developmental and tissue-specific changes in dna methylation in the vertebrate […]

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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