marge: An API for Analysis of Motifs Using HOMER in R

Abstract

Profiling of open chromatin regions through the assay for transposase-accessible chromatin (ATAC) and transcription factor binding via chromatin immunoprecipitation (ChIP) sequencing has increased our ability to resolve patterns of putative transcription factor binding sites at the genome-wide level. Popular tools such as [HOMER (http://homer.ucsd.edu/homer/) and [MEME] (http://meme-suite.org/) have driven forward the analyses of sequence composition, deriving de novo motifs and searching for the enrichment of known motifs. However, their interfaces do not allow for the construction of parallel inquiries of multiple datasets. Furthermore, their results do not conform to formats amenable to ‘tidy’ analyses, presenting a significant bottleneck in motif analysis. Here, I present ‘marge’, a companion ‘R’ package that interfaces with HOMER to facilitate the construction of queries and to tidy results for further downstream analyses.