1Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg2German Center for Cardiovascular Research (DZHK) - Partner site Heidelberg/Mannheim, 69120 Heidelberg, Germany
Checking for direct PDF access through Ovid
MotivationMetabolic 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.ResultsThe 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 implementationThe pulseR package is freely available at https://github.com/dieterich-lab/pulseR under the GPLv3.0 licence.Contacta.firstname.lastname@example.org or email@example.comSupplementary informationSupplementary data are available at Bioinformatics online.