Call for Contributions
Dear R package authors,
R has made impressive progress during the past years and has a considerable impact on the scientific community. Numerous R packages and publications emerged addressing specific use cases in the analysis of dPCR, qPCR and melting curve data. Not to forget the various data sets which come with the packages. The developed packages differ in their provided functionality ranging from specialization on a single task to complex analysis workflows. Many of them are intensively used and were published in peer-reviewed journals.
However, from a user perspective this landscape is scattered and might appear complex or limited depending on the point of view. We, the authors of R packages related to this field (see table below), attempt to publish a study of the R-qPCR landscape in a unified and open approach. We envision to describe specific aspects, data sets and examples of the packages. This will be the first publication of this kind, where the creators of the previously detached packages team up for a unified study. In a rough sketch, we envision a structure as followed for the paper:
2. R and its use in data analysis
3. R packages for the analysis of qPCR and dPCR data (contributed by package authors)
4. Use cases / What we learned from (clinical) studies
5. Glue between R packages
6. Discussion (reproducibility, ...) & outlook
Part of this study is the wish to create some "glue" (technically spoken interface) between the packages. A promising attempt has recently been started by Konstantin Blagodatskikh, who started the work on the RDML package. Given the lack of a comprehensive summary of R packages for the analysis of qPCR and dPCR data, we sincerely belief that this review fills a gap and explains users as to why R is the perfect working environment. We plan to submit the review for publication within the next six to eight months.
Stefan Rödiger (coordinator) (BTU Cottbus-Senftenberg, Germany), Stephan Pabinger (AIT, Austria), Michał Burdukiewicz (University of Wroclaw, Poland), Andrej-Nikolai Spieß (University Medical Center Hamburg-Eppendorf, Germany), Albert Kriegner (AIT, Austria)
P.S.: While we were aggregating information about the R-qPCR landscape, we noticed, even among us heavy users/developers, a lack of knowledge about some packages. For example, a set of tools is available from CRAN, Bioconductor or GitHub. Therefore, we would like to encourage everybody to suggest projects we missed. Attached you will find a table containing the projects and package authors currently addressed with this invitation.
"R as an In-Silico Ecosystem for the Systematic Analysis and Data Management of MCA, qPCR and dPCR Experiments".
|Mikhall V. Matz||USA||Yes||MCMC.qpcr||x|
|Jitao David Zhang||Switzerland||Yes||ddCt||x|
|Le Pape Sylvain||France||Yes||EasyqpcR||x|
Bart KM Jacobs
|Matthew N. McCall||USA||Yes||nondetects||x|
|Jan De Neve|
|Daniel Gerhard||New Sealand||Yes||qpcrnlme|
|Sep - Oct 2014: get in touch with R package authorsUpdate: Extended to January due to delayed responses||99 %|
|Nov - Dec 2014: fix the topics||Started|
|Feb - Jul 2015:|
* start to fill R gaps ("glue between packages")* No consense about the "glue" -> Taskforce needed
|Jul 2015 - Feb 2016:Feedback request for pending papers of all contributors||Started|
|Feb 2016 - June 2016: drafts||delayed|
|June 2016 - November 2016: Submission Publication||delayed|