Difference between revisions of "R PopGen Hackathon"

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* [http://www.bioconductor.org/packages/release/BiocViews.html#___Genetics Bioconductor packages in category Genetics]
* [http://www.bioconductor.org/packages/release/BiocViews.html#___Genetics Bioconductor packages in category Genetics]
* [http://dyerlab.github.io/gstudio/ GStudio (R. Dyer)]
* [http://dyerlab.github.io/gstudio/ GStudio (R. Dyer)]
* [http://cran.r-project.org/web/packages/ff/index.html]
* [http://cran.r-project.org/web/packages/ff/index.html ff-package (big data issue)]
=== Other tools and projects ===
=== Other tools and projects ===
* [http://snpeff.sourceforge.net/ SnpEff]: Genetic variant annotation and effect prediction toolbox.
* [http://snpeff.sourceforge.net/ SnpEff]: Genetic variant annotation and effect prediction toolbox.

Revision as of 11:41, 5 November 2014

NESCent Hackathon on Population Genetics in R



  • There are many packages in R related to reading, writing, and analyzing population genetics data in R. However, not all of them are used, and while some packages (for example, Pegas and adegenet) work well together, many others do not or not enough.
  • Many of the packages do not scale well to large volume datasets, yet these are becoming increasingly common. A common base class for efficient storage of genetic data was one of the original goals of the Rgenetics package, but this was never fully implemented.
  • Beginning to end workflows are often not considered for the design or development of individual packages, but can reveal the pain points in creating complex analysis workflows that require moving data, metadata, and other state information from one package to another, and focus attention on how these problems can be addressed or lowered.
  • E.g., pegas uses a class implemented in adegenet. Vice versa for a class in ape.
  • An outcome could be an Rweave file that walks the analysis workflow from start to end. Could also be published then.
  • There are package dependencies that are deprecated (genetics for example). Could put together some key people, and either resurrect genetics package, or develop an alternative.
  • Core packacke that provides core classes and is scalable data structures would be a great target.

Specific objectives

The event aims to target the following broad objectives. Participants will identify specific objectives and coding targets prior to and during the event.

  1. A common base class for efficient storage of genetic data.
  2. Increase interoperability between the many population genetics-related packages.
  3. Improve scalability for big data among population genetics packages.
  4. Develop a Vignette document (Rnw or Rmd) that works provides an example work-flow exercising the key packages.

All code and documentation from the hackathon will be made available immediately and freely to the community under an open-source (OSI-approved) license.


Participation will be arranged through an open Call for Participation.


Organizing Committee

  • Thibaut Jombart, Hilmar Lapp, Stéphanie Manel, Emmanuel Paradis, Bastian Pfeifer, Greg Warnes
  • Vince Carey, a core developer of Bioconductor, has agreed to serve in an advisory role during the planning phase of the event.


The hackathon is slated to take place March 16-20, 2015 at NESCent in Durham, North Carolina.

Organizational Activities

Detailed planning steps are outlined and documented separately. In particular, the following activities are taking place:

  • ...

Related external resources

R Packages and projects

Other tools and projects

  • SnpEff: Genetic variant annotation and effect prediction toolbox.