memes

The "memes" R package is a seamless interface to the MEME Suite, a toolkit widely used for biopolymer motif analysis. Overcoming integration challenges with popular R/Bioconductor frameworks, memes offers a "data aware" interface for efficient discriminative motif analysis workflows. It interfaces with MEME Suite tools, utilizing R/Bioconductor data structures for storing multidimensional data, ensuring quick access and manipulation. Additionally, memes provide data visualization capabilities to enhance result communication.

Topic

Sequence sites, features and motifs;ChIP-seq;Workflows;Sequence analysis;Protein structural motifs and surfaces

Detail

  • Operation: Sequence motif discovery;Sequence motif recognition;Sequence motif comparison;Peak calling

  • Software interface: Library

  • Language: R

  • License: The MIT License

  • Cost: Free

  • Version name: 1.10.0

  • Credit: The American Cancer Society, the National Institute of General Medical Sciences of the NIH.

  • Input: -

  • Output: -

  • Contact: Spencer Nystrom nystromdev@gmail.com

  • Collection: -

  • Maturity: Stable

Publications

  • Memes: an R interface to the MEME Suite
  • Nystrom SL, McKay DJ. Memes: A motif analysis environment in R using tools from the MEME Suite. PLoS Comput Biol. 2021 Sep 27;17(9):e1008991. doi: 10.1371/journal.pcbi.1008991. PMID: 34570758; PMCID: PMC8496816.
  • https://doi.org/10.1371/journal.pcbi.1008991
  • PMID: 34570758
  • PMC: PMC8496816

Download and documentation

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