Stefan Rödiger1, Michal Burdukiewicz2, Andrej-Nikolai Spiess3, Konstantin Blagodatskikh4. 1. Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany. 2. Department of Genomics, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland. 3. Department of Andrology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany. 4. Evrogen JSC, Moscow, Russia.
Abstract
MOTIVATION: Reproducibility, a cornerstone of research, requires defined data formats, which include the setup and output of experiments. The real-time PCR data markup language (RDML) is a recommended standard of the minimum information for publication of quantitative real-time PCR experiments guidelines. Despite the popularity of the RDML format for analysis of quantitative PCR data, handling of RDML files is not yet widely supported in all PCR curve analysis softwares. RESULTS: This study describes the open-source RDML package for the statistical computing language R. RDML is compatible with RDML versions ≤ 1.2 and provides functionality to (i) import RDML data; (ii) extract sample information (e.g. targets and concentration); (iii) transform data to various formats of the R environment; (iv) generate human-readable run summaries; and (v) to create RDML files from user data. In addition, RDML offers a graphical user interface to read, edit and create RDML files. AVAILABILITY AND IMPLEMENTATION: https://cran.r-project.org/package=RDML. rdmlEdit server http://shtest.evrogen.net/rdmlEdit/. Documentation: http://kablag.github.io/RDML/. CONTACT: k.blag@yandex.ru. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: Reproducibility, a cornerstone of research, requires defined data formats, which include the setup and output of experiments. The real-time PCR data markup language (RDML) is a recommended standard of the minimum information for publication of quantitative real-time PCR experiments guidelines. Despite the popularity of the RDML format for analysis of quantitative PCR data, handling of RDML files is not yet widely supported in all PCR curve analysis softwares. RESULTS: This study describes the open-source RDML package for the statistical computing language R. RDML is compatible with RDML versions ≤ 1.2 and provides functionality to (i) import RDML data; (ii) extract sample information (e.g. targets and concentration); (iii) transform data to various formats of the R environment; (iv) generate human-readable run summaries; and (v) to create RDML files from user data. In addition, RDML offers a graphical user interface to read, edit and create RDML files. AVAILABILITY AND IMPLEMENTATION: https://cran.r-project.org/package=RDML. rdmlEdit server http://shtest.evrogen.net/rdmlEdit/. Documentation: http://kablag.github.io/RDML/. CONTACT: k.blag@yandex.ru. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.