pulseR

pulseR is a novel R package that simplifies the analysis of metabolic labeling experiments of RNA, allowing for the estimation of RNA synthesis and decay rates. It provides a comprehensive and versatile workflow that accommodates different experimental designs and incorporates negative-binomial models to better model count data. Additionally, it is the only publicly available solution containing labeled and unlabelled spike-in sets, accounting for potential labeling biases.

Topic

RNA-seq;Molecular interactions, pathways and networks;RNA

Detail

  • Operation: RNA-seq read count analysis

  • Software interface: Command-line user interface

  • Language: Javascript

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: v1.0.3

  • Credit: The Klaus Tschira Stiftung gGmbH, the German Center for Cardiovascular Research (DZHK).

  • Input: -

  • Output: -

  • Contact: Alexey Uvarovskii a.uvarovskii@uni-heidelberg.de, Christoph Dieterich christoph.dieterich@uni-heidelberg.de

  • Collection: -

  • Maturity: Stable

Publications

  • pulseR: Versatile computational analysis of RNA turnover from metabolic labeling experiments
  • Uvarovskii A, Dieterich C. pulseR: Versatile computational analysis of RNA turnover from metabolic labeling experiments. Bioinformatics. 2017 Oct 15;33(20):3305-3307. doi: 10.1093/bioinformatics/btx368. PMID: 29028260.
  • https://doi.org/10.1093/bioinformatics/btx368
  • PMID: 29028260
  • PMC: -

Download and documentation

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