R qPCR / dPCR / MCA Landscape

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:

1. Introduction
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.

Kind regards

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.

Working title

"R as an In-Silico Ecosystem for the Systematic Analysis and Data Management of MCA, qPCR and dPCR Experiments".

Participating projects

Package maintainer
Contributor
CountryAggreed
to contribute
PackageCRANBiocon-
ductor
GitHub
Claus EkstromDenmarkYeskulifex
Mikhall V. MatzUSAYesMCMC.qpcrx
Matthias KohlGermanyyesSLqPCRx
Jitao David ZhangSwitzerlandYesddCtx
Le Pape SylvainFranceYesEasyqpcRx
James PerkinsUKYesReadqPCR
NormqPCR
x
x
Andrej-Nikolai SpiessGermanyYesqpcRx
Michael Burdukiewicz

Stefan Rödiger

Bart KM Jacobs

Lieven Clement
Poland

Germany

Belgium

Belgium
YesdpcRx
Stefan Rödiger

Michael Burdukiewicz
Germany

Poland
YeschipPCR
MBmca
x
Matthew N. McCallUSAYesnondetectsx
Jan De Neve

Lieven Clement

Joris Meys

Oliver Thas
Belgium

Belgium

Belgium

Belgium
YesunifiedWMWqPCRx
Konstantin Blagodatskikh

Michal Burdukiewicz

Stefan Rödiger
Russia

Poland

Germany
YesRDMLx
Albert Kriegner

Stephan Pabinger
Austria

Austria
Yes.
Daniel GerhardNew SealandYesqpcrnlme
qpcrmix
x
x

Milestones

TaskCompleted
Sep - Oct 2014: get in touch with R package authorsUpdate: Extended to January due to delayed responses99 %
Nov - Dec 2014: fix the topicsStarted
40 %
Feb - Jul 2015:
* start to fill R gaps ("glue between packages")* No consense about the "glue" -> Taskforce needed
Started
10 %
Jul 2015 - Feb 2016:Feedback request for pending papers of all contributorsStarted
Feb 2016 - June 2016: draftsdelayed
June 2016 - November 2016: Submission Publicationdelayed

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