A package containing an extended version of the original GADEM C code. For ChIP-Seq data, a key improvement is that, on multicore computers, rGADEM can take advantage of multithreading via Grand Central Dispatch on Mac OS X 10.6 and above, and openMP on other Unix platforms, to sharply reduce run times. It can also prioritize sequences with large ChIP enrichments and includes novel prior distributions that prioritize for motif occurrences that are nearer to sequence (peak) centers. Such prior settings can potentially improve the detection of primary motifs at the cost of missing secondary motifs that can be present at low enrichment and/or further away for the center. rGADEM is an efficient motif discovery tool for large-scale genomic sequence data. It provides a complete set of Bioconductor tools for sequence and motif analysis of ChIP-seq and ChIP-chip data.