PulseR: Versatile computational analysis of RNA turnover from metabolic labeling experiments

Abstract

Motivation Metabolic labelling of RNA is a well-established and powerful method to estimate RNA synthesis and decay rates. The pulseR R package simplifies the analysis of RNA-seq count data that emerge from corresponding pulse-chase experiments. Results The pulseR package provides a flexible interface and readily accommodates numerous different experimental designs. To our knowledge, it is the first publicly available software solution that models count data with the more appropriate negative-binomial model. Moreover, pulseR handles labelled and unlabelled spike-in sets in its workflow and accounts for potential labeling biases (e.g. number of uridine residues). Availability and implementation The pulseR package is freely available at https://github.com/dieterich-lab/pulseR under the GPLv3.0 licence. Contact a.uvarovskii@uni-heidelberg.de or christoph.dieterich@uni-heidelberg.de Supplementary informationSupplementary dataare available at Bioinformatics online.