==== AREM ====


==AREM: Aligning ChIP-seq reads by Expectation-Maximization.==


== Description ==


AREM takes the classic peak calling algorithm used in MACS 1.4 (including an empirically optimal tag shift and a locally-adjusted poissonian statistical model for tag enrichment) and adds a component for realigning ambigously mapping reads.  A probabilistic model assigns reads to regions that are more likely to be peaks (having higher enrichment).


== Paper ==


For additional information, see our paper in RECOMB 2011 (D Newkirk, J Biesinger, A Chon, K Yokomori, X Xie, 2011) or download a copy [[http://www.ics.uci.edu/~xhx/publications/arem_recomb.pdf|here]].


== Code ==


Regular releases of the software are pushed to the sourceforge page: [[http://sourceforge.net/projects/arem/|http://sourceforge.net/projects/arem/]]


The development version of the code is available at: [[https://github.com/jakebiesinger/AREM|https://github.com/jakebiesinger/AREM]]