[BioC] 'SRAdb useful for visualizing BAM files'

[Sean Davis]

On Fri, Apr 9, 2010 at 9:40 PM, Paul Shannon
<pshannon at systemsbiology.org> wrote:
> Martin suggests  ("An Introduction to Rsamtools", April 8th, 2010):
>
>   'Users might also find the interface to the integrative genome browser (IGV) in SRAdb useful for visualizing BAM files.'
>
> I have tried googling many versions of the relevant words, and cannot find anything about this.  Is it an R interface to IGV?  Any ideas about how I can find out more?
>
> Thanks!

Hi, Paul.

SRAdb is an R package for searching the NCBI SRA database in a more
user-friendly way and for accessing the data in SRA.  One of the
facilities that is included is an interface to start IGV and load BAM
files of interest directly from R.  The package has been submitted to
bioconductor and is in review.  However, if you like, you can
potentially install it now (assuming that you can deal with source
package installation) by doing:

install.packages('SRAdb',repos='http://watson.nci.nih.gov/R/repos',type='source')

There is a vignette included.

Sean