Imports real-time thermo cycler (qPCR) data from Real-time PCR Data Markup Language (RDML) and transforms to the appropriate formats of the 'qpcR' and 'chipPCR' packages. Contains a dendrogram visualization for the structure of RDML object and GUI for RDML editing.
The RDML package is published in Oxford Bioinformatics:
Stefan Rödiger, Michał Burdukiewicz, Andrej-Nikolai Spiess, Konstantin Blagodatskikh; Enabling reproducible real-time quantitative PCR research: the RDML package, Bioinformatics, https://doi.org/10.1093/bioinformatics/btx528 (see also
The stable version of the
RDML package for R is hosted on CRAN and can be installed as any R package.
You can install the latest development version of the code using the
devtools R package.
# Install devtools, if you haven't already.install.packages("devtools")library(devtools)install_github("kablag/RDML")
The manual is available online.
RDML imports various data formats (CSV, XMLX) besides the RDML format. Provided that the raw data
have a defined structure (as described in the vignette) the import should be
done by a few clicks. The example below shows the import of amplification curve
data, which were stored in a CSV file. The function
rdmlEdit() was used in the
RKWard IDE/GUI for further processing. rdmlEdit may be also accessed as a web server (http://shtest.evrogen.net/rdmlEdit/).
Once imported enables
rdmlEdit() and other functions from the
RDML package complex
data visualization and processing in the R statistical computing environment.