R and .NET Bio

Coordinator
Aug 3, 2012 at 11:32 PM

This is something I have been wondering about for a while. There are a few links that might make such a thing possible, including the existing RDotNet project here http://rdotnet.codeplex.com/. This project manages a number of dependencies in a clean fashion, allowing you to get started by just referencing a single DLL. 

But this post is prompted by a tweet from @dsyme posting a link to an F# type provider for R built on top of this project. The code is in its infancy, but this is the sort of bridge that might just allow a clean mix of tools and technologies: 

  • functional syntax for quickly setting up data extraction and parsing, maybe applying some transformations across the collection 
  • the .NET Bio libraries to do all that stuff efficiently, and to store the resulting objects in well-chosen data structures. 
  • ready integrated access to R to do specific data analysis and ML. 

Has anyone out there tried to get .NET Bio Sequence objects to play nicely with R and Bioconductor? 

The post referred to is here: 

http://blogs.msdn.com/b/dsyme/archive/2012/08/03/access-statistical-packages-from-r-with-f-3-0.aspx

The code example isn't very viewable, so I went to the github repo. The example is very clear: 

https://github.com/BlueMountainCapital/FSharpRProvider

https://github.com/BlueMountainCapital/FSharpRProvider/blob/master/example.fsx

 

Anyone interested in pursuing this? 

 

cheers

jh

Aug 6, 2012 at 4:01 PM

How about Sho? (http://msdn.microsoft.com/en-us/devlabs/gg585581.aspx)

Coordinator
Aug 15, 2012 at 5:23 AM

sorry for the delay. I looked at this the day after you sent it and then got busy. It seems a very good project, but I tend to feel that R has such a community behind it that if we were to focus our attention in the one area, R would be a better choice. It just has so much traction, and so many libraries. 

It will be interesting to see what sort of uses people make of the F# and R links, however, and of course it would be good to see some more contributions to this and the other future threads. 

cheers

jh