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

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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 information

Supplementary data are available at Bioinformatics online.

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