Document Actions

The Rgenetics Project Website

by rerla — last modified 2007-12-14 13:26

Rgenetics: statistical and population genetics for Bioconductor

R Genetics Project

The R Genetics Project is an open-source project, which solicits contributions in a community-supported, collaborative effort to provide the data structures and analytic tools needed for the management, visualization, exchange and analysis of genetic data. Our focus is currently on building the basic representation and annotation infrastructure for a coherent framework and the project is still very much under construction.

Quickstart for Users

Install a recent version of R
Download the install script by executing the following commands in R:
```
       source("http://bioconductor.org/biocLite.R")
```

Install the R-Genetics packages:

       biocLite( c('GeneticsBase', 'GeneticsDesign', 'GeneticsPed', 'fbat') )

Look at the list of available tutorial vignettes:

       vignette(package=c('GeneticsBase', 'GeneticsDesign', 'GeneticsPed', 'fbat'))

Join the mailing list
Have fun!

QuickStart for Developers:

Checkout the current release from BioC or if you prefer living dangerously, the current development code from svn
Poke at the code and help us make it better.
Browse the mail-list archives
Submit tickets
Join the mailing list
Join the teleconference 2nd and 4th Fridays of each month at 1:30pm EST Toll Free Dial In Number: (877)232-4392 Participant code: 985999

Project Goals

We are working in a coordinated way although statistical genetics methods developers are welcome to propose extensions which they are willing to take responsibility for. The first focus for the core developers is on developing robust and efficient data structures which are capable of supporting the majority of common analyses. At the same time, we are testing and refining this framework by providing high-quality and useful applications. In particular, we are trying to figure out how to efficiently support large scale whole-genome SNP chip based association studies, since many of the core developers are working or will soon be working with those datasets

Licensing

The code produced by the core developer collaboration will be released under the terms of the Lesser GNU Public License. Some pre-existing code may be released under more or less resistrictive license terms in order to meet legal requirements or the preferences of the contributors. We ask developers to adopt the LGPL or some other open-source license which commercial providers can work with since we welcome and encourage participation from commercial organizations willing to work with us, preferably on some mutually beneficial basis.

Governance

The open-source project

Currently managed in an open, negotiated process by a small core committee of working developers:

Current members in alphabetic order:

Scott D Chasalow "scott dot chasalow at bms dot com", Bristol-Myers Squibb
Junsheng Cheng "jcheng8 at users dot sourceforge dot net", Univ. Chicago
Nitin Jain "Nitin Jain at bms dot com", Bristol-Myers Squibb
Gregor Gorjanc "gregor.goranjanc at bfro dot uni-lj dot si", University of Ljubljana
David Henderson "dhenderson at insightful dot com", Insightful
Ross Lazarus "ross dot lazarus at channing dot harvard dot edu", Channing Laboratory
Giovanni Montana "giovanni dot montana at bms dot com", Bristol-Myers Squibb
Michael O'Connell "moconnell at insightful dot com", Insightful
Gregory Warnes "greg dot warnes at warnes dot net", University of Rochester, and Random Technologies, LLC.

In time, a larger advisory group including users and package maintainers will be accumulated.

R01 grant

Ross Lazarus is the principal investigator on an R01 grant from the NIH. Co-investigators on this grant include Vince Carey, Robert Gentleman, Nan Laird, Christoph Lange, Greg Warnes and Xin Xu. The grant provides some small dedicated programming and documentation writing resources which are being used to support the open-source project.