I have a list of DE transcripts emerging from an analysis of RNA-seq data. I have mapped these transcripts back to their Ensembl ENSG IDs for submission to the `findMotifs.pl` function in the `HOMER` software suite http://homer.ucsd.edu/homer/microarray/index.html.
As described by the link, the goal of `findMotifs.pl` is to extract the promoter region of each gene and look for transcription factor binding motifs that are disproportionately represented in the list of named genes above background levels. As others have described, I am finding this software to be a bit buggy and would much rather use something in Bioconductor that has better documentation/ user community/ version support. Is there any integrated Bioconductor solution to accomplish the analyses described here?