memes

memes provides an R interface to the MEME Suite for motif analysis of DNA, RNA, and protein sequences.

Key Features:

• R/Bioconductor integration: Executes MEME Suite motif analysis tasks within R and integrates results with Bioconductor data structures.
• Motif analysis support: Supports motif matching, motif comparison, and de novo motif discovery using MEME Suite tools.
• Data storage and manipulation: Stores and manipulates complex, multidimensional MEME Suite outputs using R/Bioconductor data structures.
• Visualization: Generates visualizations of motif analysis results.
• Containerized environment: Provides a Docker container built from the development branch of bioconductor_docker_meme that includes the memes package and dependencies.

Scientific Applications:

• Motif discovery: De novo identification of sequence motifs in DNA, RNA, or protein sequences using MEME Suite algorithms.
• Motif matching: Detection of occurrences of known motifs in biological sequences via MEME Suite matching tools.
• Motif comparison: Comparison of motif models to evaluate similarity and relationships between motifs.
• Discriminative motif analysis: Support for discriminative analyses across sample groups using Bioconductor data structures.

Methodology:

Interfaces with MEME Suite tools from R to execute motif matching, comparison, and de novo discovery; maps MEME Suite outputs to Bioconductor data structures for storage and manipulation; generates motif visualizations; includes a Docker container built from the bioconductor_docker_meme development branch containing the package and dependencies.