TY - JOUR T1 - <em>RiboDiff:</em> Detecting Changes of Translation Efficiency from Ribosome Footprints JF - bioRxiv DO - 10.1101/017111 SP - 017111 AU - Yi Zhong AU - Theofanis Karaletsos AU - Philipp Drewe AU - Vipin Sreedharan AU - Kamini Singh AU - Hans-Guido Wendel AU - Gunnar Rätsch Y1 - 2015/01/01 UR - http://biorxiv.org/content/early/2015/04/10/017111.abstract N2 - Motivation Deep sequencing based ribosome footprint profiling can provide novel insights into the regulatory mechanisms of protein translation. However, the observed ribosome profile is fundamentally confounded by transcriptional activity. In order to decipher principles of translation regulation, tools that can reliably detect changes in translation efficiency in case-control studies are needed.Results We present a statistical framework and analysis tool, RiboDiff, to detect genes with changes in translation efficiency across experimental treatments. RiboDiff uses generalized linear models to estimate the over-dispersion of RNA-Seq and ribosome profiling measurements separately, and performs a statistical test for differential translation efficiency using both mRNA abundance and ribosome occupancy.Availability Source code and documentation are available at http://github.com/ratschlab/ribodiff. Supplementary Material can be found at http://bioweb.me/ribodiff.Contact zhongy{at}cbio.mskcc.org and raetsch{at}cbio.mskcc.org. ER -