Methylation plotter statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Methylation plotter
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Tool usage distribution map

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Associated diseases

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Protocols

Methylation plotter specifications

Information


Unique identifier OMICS_04865
Name Methylation plotter
Interface Web user interface
Restrictions to use None
Programming languages R
License GNU General Public License version 2.0
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Izaskun Mallo

Publication for Methylation plotter

Methylation plotter citations

 (6)
library_books

CpG location and methylation level are crucial factors for the early detection of oral squamous cell carcinoma in brushing samples using bisulfite sequencing of a 13 gene panel

2017
Clin Epigenetics
PMCID: 5558660
PMID: 28814981
DOI: 10.1186/s13148-017-0386-7

[…] TGA4, MIR193), whereas three were hypomethylated (GP1BB, MIR296, TERT) in OSCC/HGSIL. Additional file depicts the mean methylation level for each group of the interrogated genes visualized using the Methylation plotter tool [] and the Kruskal-Wallis test for single CpG. Figure shows the fluctuating methylation level among different CpGs evaluated in GP1BB and ZAP70. Mean methylation level and co […]

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Genome wide DNA methylation landscape defines specialization of regulatory T cells in tissues

2017
Nat Immunol
PMCID: 5912503
PMID: 28783152
DOI: 10.1038/ni.3799
call_split See protocol

[…] ise average linkage clustering. No normalizations or transformations have been performed. Heatmaps were generated with gene pattern software/heatmap viewer. Methylation plots (, ) were generated with methylation plotter. […]

library_books

Small Magnitude Effect Sizes in Epigenetic End Points are Important in Children’s Environmental Health Studies: The Children’s Environmental Health and Disease Prevention Research Center’s Epigenetics Working Group

2017
Environ Health Perspect
PMCID: 5382002
PMID: 28362264
DOI: 10.1289/EHP595

[…] ches implemented depend on the type of data analyzed.R packages that can implement some of all of the above include MethVisual (), methyAnalysis (version 1.12.0; R Project for Statistical Computing), Methylation plotter (), MethTools (), MethylMix (), IMA (), coMET (), and minfi () (). Most of these enable implementation of site-level as well as region-level DNA methylation analysis based on the 4 […]

library_books

Profiling genome wide DNA methylation

2016
PMCID: 4926291
PMID: 27358654
DOI: 10.1186/s13072-016-0075-3

[…] hat supports the local alignment and computational removal of potentially unconverted reads. The alignment profile can be visualized with tools such as the UCSC genome browser [], WBSA [], IGV [] and Methylation plotter [], which results in greater clarity at a single-base resolution across the genome. […]

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Muscle cell identity requires Pax7 mediated lineage specific DNA demethylation

2016
BMC Biol
PMCID: 4831197
PMID: 27075038
DOI: 10.1186/s12915-016-0250-9
call_split See protocol

[…] rated by the ENCODE Project Consortium []. GEO accession numbers are listed in Additional file . Sodium bisulphite sequencing data and Kruskal-Wallis test of sodium bisulphite data were done with the Methylation Plotter web tool []. Supporting data containing the individual gene expression values are shown in Additional file . […]

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Ddx1 knockout results in transgenerational wild type lethality in mice

2015
Sci Rep
PMCID: 4408975
PMID: 25909345
DOI: 10.1038/srep09829
call_split See protocol

[…] 3 reverse sequencing primer (5’-CAGGAAACAGCTATGAC). DNA sequences were then subjected to analysis by Bisulfite Sequencing DNA Methylation Analysis (BISMA) using default parameters and displayed using Methylation plotter. […]


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Methylation plotter institution(s)
Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Ctra de Can Ruti, camí de les escoles,Badalona, Spain

Methylation plotter review

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evelyne segal

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Web
Methylation plotter is a user-friendly tool to build publication ready figures for the visualization of DNA methylation data. It can also be used for visualization of NOMEseq analysis (Nucleosome occupancy and methylation data). Different kinds of visualization can be selected (Box plots, methylation profiling, clustering.....). Statistics are also available. The tool is very easy to use.
The last star would have been selected if it had been possible to choose to change the design of the plots (colors...).