RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints

We present a statistical framework and an 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 and Implementation: RiboDiff webpage http://bioweb.me/ribodiff. Source code including scripts for preprocessing the FASTQ data are available at http://github.com/ratschlab/ribodiff.
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Supplementary information: Supplementary data are available at Bioinformatics online.

Source: Bioinformatics - December 28, 2016 Category: Bioinformatics Authors: Zhong, Y., Karaletsos, T., Drewe, P., Sreedharan, V. T., Kuo, D., Singh, K., Wendel, H.-G., Rätsch, G. Tags: GENE EXPRESSION Source Type: research