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Title (Primary) R as an environment for the reproducible analysis of DNA amplification experiments
Author Rödiger, S.; Burdukiewicz, M.; Blagodatskikh, K.; Jahn, M.; Schierack, P.;
Journal R Journal
Year 2015
Department UMB;
Volume 7
Issue 1
Language englisch;
POF III (all) T41;
UFZ wide themes RU3;
Abstract There is an ever-increasing number of applications, which use quantitative PCR (qPCR) or digital PCR (dPCR) to elicit fundamentals of biological processes. Moreover, quantitative isothermal amplification (qIA) methods have become more prominent in life sciences and point-of-care- diagnostics. Additionally, the analysis of melting data is essential during many experiments. Several software packages have been developed for the analysis of such datasets. In most cases, the software is either distributed as closed source software or as monolithic block with little freedom to perform highly customized analysis procedures. We argue, among others, that R is an excellent foundation for reproducible and transparent data analysis in a highly customizable cross-platform environment. However, for novices it is often challenging to master R or learn capabilities of the vast number of packages available. In the paper, we describe exemplary workflows for the analysis of qPCR, qIA or dPCR experiments including the analysis of melting curve data. Our analysis relies entirely on R packages available from public repositories. Additionally, we provide information related to standardized and reproducible research.
ID 16369
Persistent UFZ Identifier
Rödiger, S., Burdukiewicz, M., Blagodatskikh, K., Jahn, M., Schierack, P. (2015):
R as an environment for the reproducible analysis of DNA amplification experiments
R Journal 7 (1), 127 - 150