Memes: A motif analysis environment in R using tools from the MEME Suite.

Identification of biopolymer motifs represents a key step in the analysis of biological sequences. The MEME Suite is a widely used toolkit for comprehensive analysis of biopolymer motifs; however, these tools are poorly integrated within popular analysis frameworks like the R/Bioconductor project, c...

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Autores principales:	Spencer L Nystrom, Daniel J McKay
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/fbc84a12ed224762bdcec2056ca00705
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id	oai:doaj.org-article:fbc84a12ed224762bdcec2056ca00705
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spelling	oai:doaj.org-article:fbc84a12ed224762bdcec2056ca007052021-12-02T19:58:13ZMemes: A motif analysis environment in R using tools from the MEME Suite.1553-734X1553-735810.1371/journal.pcbi.1008991https://doaj.org/article/fbc84a12ed224762bdcec2056ca007052021-09-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.1008991https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Identification of biopolymer motifs represents a key step in the analysis of biological sequences. The MEME Suite is a widely used toolkit for comprehensive analysis of biopolymer motifs; however, these tools are poorly integrated within popular analysis frameworks like the R/Bioconductor project, creating barriers to their use. Here we present memes, an R package that provides a seamless R interface to a selection of popular MEME Suite tools. memes provides a novel "data aware" interface to these tools, enabling rapid and complex discriminative motif analysis workflows. In addition to interfacing with popular MEME Suite tools, memes leverages existing R/Bioconductor data structures to store the multidimensional data returned by MEME Suite tools for rapid data access and manipulation. Finally, memes provides data visualization capabilities to facilitate communication of results. memes is available as a Bioconductor package at https://bioconductor.org/packages/memes, and the source code can be found at github.com/snystrom/memes.Spencer L NystromDaniel J McKayPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 17, Iss 9, p e1008991 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Spencer L Nystrom Daniel J McKay Memes: A motif analysis environment in R using tools from the MEME Suite.
description	Identification of biopolymer motifs represents a key step in the analysis of biological sequences. The MEME Suite is a widely used toolkit for comprehensive analysis of biopolymer motifs; however, these tools are poorly integrated within popular analysis frameworks like the R/Bioconductor project, creating barriers to their use. Here we present memes, an R package that provides a seamless R interface to a selection of popular MEME Suite tools. memes provides a novel "data aware" interface to these tools, enabling rapid and complex discriminative motif analysis workflows. In addition to interfacing with popular MEME Suite tools, memes leverages existing R/Bioconductor data structures to store the multidimensional data returned by MEME Suite tools for rapid data access and manipulation. Finally, memes provides data visualization capabilities to facilitate communication of results. memes is available as a Bioconductor package at https://bioconductor.org/packages/memes, and the source code can be found at github.com/snystrom/memes.
format	article
author	Spencer L Nystrom Daniel J McKay
author_facet	Spencer L Nystrom Daniel J McKay
author_sort	Spencer L Nystrom
title	Memes: A motif analysis environment in R using tools from the MEME Suite.
title_short	Memes: A motif analysis environment in R using tools from the MEME Suite.
title_full	Memes: A motif analysis environment in R using tools from the MEME Suite.
title_fullStr	Memes: A motif analysis environment in R using tools from the MEME Suite.
title_full_unstemmed	Memes: A motif analysis environment in R using tools from the MEME Suite.
title_sort	memes: a motif analysis environment in r using tools from the meme suite.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/fbc84a12ed224762bdcec2056ca00705
work_keys_str_mv	AT spencerlnystrom memesamotifanalysisenvironmentinrusingtoolsfromthememesuite AT danieljmckay memesamotifanalysisenvironmentinrusingtoolsfromthememesuite
_version_	1718375818055385088

Memes: A motif analysis environment in R using tools from the MEME Suite.

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