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 in publications

 (5)
PMCID: 5558660
PMID: 28814981
DOI: 10.1186/s13148-017-0386-7

[…] in parallel, we used perl to create single specific files for every interrogated gene, which were then visualized using biq analyzer [], quma [], and bisma [] to confirm data from bspat analysis. methylation plotter (http://gattaca.imppc.org:3838/methylation_plotter/) [] was used to create fig. and additional file ., multiclass linear discriminant analysis and receiver operating […]

PMCID: 5912503
PMID: 28783152
DOI: 10.1038/ni.3799

[…] 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., sorted cell populations were lysed and rna was isolated using the rneasy mini kit (quiagen). synthesis of cdna was performed with superscript reverse transcriptase ii […]

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

[…] 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.table 2 brat-bw bisulfite-treated reads analysis tool (burrows–wheeler transform), ucsc genome […]

PMCID: 4831197
PMID: 27075038
DOI: 10.1186/s12915-016-0250-9

[…] 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 ., additional file 1: additional file 2: additional file 3: […]

PMCID: 4408975
PMID: 25909345
DOI: 10.1038/srep09829

[…] 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., mh, em and mb generated the data. mh and dg performed the data analysis and constructed the figures. mh, dg and rg wrote the main manuscript text. all authors reviewed […]


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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...).