pulseR

• Verfasst von: Uvarovskii, Alexey [VerfasserIn]
• Verfasst von: Dieterich, Christoph [VerfasserIn]
• Titel: pulseR
• Titelzusatz: versatile computational analysis of RNA turnover from metabolic labeling experiments
• Verf.angabe: Alexey Uvarovskii and Christoph Dieterich
• Umfang: 3 S.
• Fussnoten: Gesehen am 28.08.2018 ; Advance Access Publication Date: 24 June 2017
• Titel Quelle: Enthalten in: Bioinformatics
• Jahr Quelle: 2017
• Band/Heft Quelle: 33(2017), 20, S. 3305-3307
• ISSN Quelle: 1367-4811
• DOI: doi:10.1093/bioinformatics/btx368
• Datenträger: Online-Ressource
• Sprache: eng
• K10plus-PPN: 1580462782

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).