pulseR：基于代谢标记实验的 RNA 周转的多功能计算分析。
pulseR: Versatile computational analysis of RNA turnover from metabolic labeling experiments.
机构信息
Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg.
German Center for Cardiovascular Research (DZHK) - Partner site Heidelberg/Mannheim, 69120 Heidelberg, Germany.
出版信息
Bioinformatics. 2017 Oct 15;33(20):3305-3307. doi: 10.1093/bioinformatics/btx368.
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.
动机
RNA 的代谢标记是一种成熟且强大的方法，可用于估计 RNA 合成和降解速率。pulseR R 包简化了来自相应脉冲追踪实验的 RNA-seq 计数数据的分析。
结果
pulseR 包提供了一个灵活的接口，并易于适应许多不同的实验设计。据我们所知，它是第一个公开可用的软件解决方案，它使用更合适的负二项式模型对计数数据进行建模。此外，pulseR 在其工作流程中处理标记和未标记的 Spike-in 集，并考虑潜在的标记偏差（例如尿嘧啶残基的数量）。
可用性和实现
pulseR 包可在 https://github.com/dieterich-lab/pulseR 上免费获得，许可证为 GPLv3.0。
联系人
a.uvarovskii@uni-heidelberg.de 或 christoph.dieterich@uni-heidelberg.de。
补充信息
补充数据可在 Bioinformatics 在线获得。
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