MetaPlotR protocols

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MetaPlotR specifications

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Unique identifier OMICS_17014
Name MetaPlotR
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl, R
Computer skills Advanced
Stability Stable
Requirements
ggplot2, scales, perl, bedtools
Maintained Yes

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  • person_outline Samie Jaffrey <>

Publication for MetaPlotR

MetaPlotR in pipeline

2017
PMCID: 5677536
PMID: 28920958
DOI: 10.1038/nm.4416

[…] reported previously. the total utpm were summed across the entire gene length and used to generate a rank list of miclip reads per gene., metagenes were constructed for the called m6 a sites using metaplotr. in brief, drach sites were mapped to different rna features (5′ utr, cds and 3′ utr) of the human genome (hg19). the position of the sites was normalized to the median feature length […]

MetaPlotR in publications

 (2)
PMCID: 5677536
PMID: 28920958
DOI: 10.1038/nm.4416

[…] reported previously. the total utpm were summed across the entire gene length and used to generate a rank list of miclip reads per gene., metagenes were constructed for the called m6 a sites using metaplotr. in brief, drach sites were mapped to different rna features (5′ utr, cds and 3′ utr) of the human genome (hg19). the position of the sites was normalized to the median feature length […]

PMCID: 5703642
PMID: 29087293
DOI: 10.7554/eLife.26116.050

[…] sliding windows and calculating an enrichment score for each sliding window (). homer software package () was used for de novo discovery of the methylation motif. metagene was generated using the metaplotr package ()., libraries were separated by barcode, matching reads were collapsed and barcodes removed. for all libraries, single-end rna-seq reads were mapped to the mouse (mm9 assembly) […]

MetaPlotR institution(s)
Department of Pharmacology, Weill Medical College, Cornell University, New York, NY, USA
MetaPlotR funding source(s)
Supported by NIH grant R01DA037755 and in part by National Cancer Institute (NCI) Grant NIH T32 CA062948 and by a Postdoctoral Enrichment Program Award from the Burroughs Wellcome Fund.

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