motifTestR: A Bioconductor package for the analysis of transcription factor binding motifs in sequence data

Background: The analysis of sequence motifs is a fundamental step in much transcription factor research and the package motifTestR, as presented here, provides comprehensive methods for motif analysis. As well as core infrastructure for selecting and simulating background sequences and visualisation of results, the package allows for the analysis of motif enrichment and positional bias, including analysis of motifs by cluster. The package is built natively in R, removing any requirement for external software, and is designed to integrate smoothly within the Bioconductor ecosystem. Results: Here the package is benchmarked against two key tools within the MEME Suite, \textit{ame} and \textit{centrimo}, with results showing comparable, and in some cases improved, performance when compared to these tools. The package additionally enables the selection of more suitable background sequences for enrichment analysis. Conclusion: motifTestR provides a convenient and robust tool for testing motif enrichment within sets of sequences, representing an important, R-native addition able to be easily incorporated into Bioconductor-based workflows and analyses.