I'm looking for methods and/or tools that can be used to assess overlap between ChIP (ChIP-ChIP or ChIP-Seq) datasets.
Being a drosophilist I have access to several ChIP datasets at modENCODE and BDTNP and I'd like to know if some of these transcription factor binding profiles show a significant overlap with the one I produced for my transcription factor of interest. The idea is to make hypotheses about possible cofactors.
Bonus points if the tools also help in the visualisation of the overlap and significance and if they're R or Bioconductor-related.
What are your suggestions Biostar?
Thanks a lot,