We have just released Version 1.0 of ChIPseeqer, a comprehensive framework for analysis of ChIP-seq data. ChIPseeqer contains a very fast and accurate ChIP-seq peak detection program, as well as several others tools to facilitate regulatory element discovery using FIRE, pathway analysis using iPAGE and conservation analyses.
http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml
Following a request from somebody at Virginia Tech, we have added Rice to the list of organisms supported by FIRE. We used the following gene identifiers:
LOC_Os11g37320
LOC_Os01g12410
LOC_Os01g25110
LOC_Os02g07360
LOC_Os11g45360
etc.
To analyze Rice expression data, you’ll need to download FIRE, then download the rice_data.zip file. The download site is http://tavazoielab.princeton.edu/FIRE/
