[BioC] Chromosome view of Nimblegen data

Sean Davis sdavis2 at mail.nih.gov
Thu Dec 14 21:20:06 CET 2006

On Thursday 14 December 2006 14:43, Rustici, Gabriella (NIH/NCI) [F] wrote:
> Hi all,
> Is there a Bioconductor package I could use to visualize Nimblegen
> ChIP-chip data?
> I'd like to do a whole genome plot showing chromosome location of
> enriched genes for the TF of interest.
> Could I use "geneplotter" to do it?

You probably could.  However, you might want to look into using the Affymetrix 
Integrated Genome Browser (IGB) for visualizing your ChIP/chip data.  It 
takes as input simple text files for visualization purposes.  It is a Java 
program, so runs fine on windows, linux, and Macos.  

As an aside, I have an R package for chip/chip analysis that is available 


It includes functionality to load the nimblegen GFF files, calculate some 
stats for each probe, and then export the results and raw data for viewing in 
the Affy IGB.  It is still very much under development, so I would appreciate 
any feedback if you decide to use it.


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