This shows you the differences between two versions of the page.
| Next revision | Previous revision | ||
|
software:arem [2013/02/21 15:02] wbiesing created |
software:arem [2013/04/16 21:15] (current) wbiesing |
||
|---|---|---|---|
| Line 1: | Line 1: | ||
| ==== AREM ==== | ==== AREM ==== | ||
| - | AREM: Aligning ChIP-seq reads by Expectation-Maximization. | + | |
| + | |||
| + | ==AREM: Aligning ChIP-seq reads by Expectation-Maximization.== | ||
| + | |||
| == Description == | == 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). | 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 == | == 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]]. | 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 == | == Code == | ||
| - | Regular releases of the software are pushed to the sourceforge page: | ||
| - | [[http://sourceforge.net/projects/arem/]] | ||
| - | The development version of the code is available at: | + | |
| - | [[https://github.com/jakebiesinger/AREM]] | + | 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]] | ||