R help - May 2006 - Bioconductor AND Genetics Library

I am aware of the R Genetics Project that developed the R library and 
software called Bioconductor (http://www.bioconductor.org/ ) . How do the 
two relate to each other? What is the one that the other is not and vice 
versa? Can anybody link me to something that answers the question?

-- 
Farrel Buchinsky, MD
Pediatric Otolaryngologist
Allegheny General Hospital
Pittsburgh, PA

On Sat, 13 May 2006, Farrel Buchinsky wrote:
> I am aware of the R Genetics Project that developed the R library and
> software called Bioconductor (http://www.bioconductor.org/ ) . How do the
> two relate to each other? What is the one that the other is not and vice
> versa? Can anybody link me to something that answers the question?
The genetics project is primarily about inherited DNA polymorphisms.

Bioconductor primarily isn't -- it has a lot of RNA expression analysis 
tools, infrastructure such as interactive graphics, links to online genome 
databases, graph algorithms, and the DNA stuff that it has tends more 
towards copy number/loss of heterozygosity analysis for cancer.

Bioconductor is also a lot further along.

 	-thomas

Not much to add over what Thomas already reported. Some folks are 
involved in both projects and we are certainly going to reuse as much 
code as possible (in particular I think that progress is already being 
made on SNP arrays).

Some of the distinction is to demonstrate clear focus for the projects, 
and I hope that there will be other projects aimed at other types of 
biological problems in the future and that the main designers and 
developers of those projects also work towards integration with existing 
code, which is one of the goals here. As it becomes clearer what sorts 
of things work, what experiments are being carried out, I hope we move 
towards common data formats and some infrastructure that can be reused 
by other developers.

There is no reason that there be one particular download site, and 
indeed lots of reasons to separate things out. Some of the tools needed 
for users to manage different repositories are now in place in R, and I 
suspect that they will mature and user experiences will become simpler.

We are also working on the biocViews tools (like CRAN task views but 
also pretty different from that approach) that will make it easier for 
users to navigate the existing 170 packages in Bioconductor now.

best wishes
   Robert


Farrel Buchinsky wrote:
> I am aware of the R Genetics Project that developed the R library and 
> software called Bioconductor (http://www.bioconductor.org/ ) . How do the 
> two relate to each other? What is the one that the other is not and vice 
> versa? Can anybody link me to something that answers the question?
> 
-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org