[BioC] What happened to GenomicFeatures::spliceGraph?

[Martin Morgan]

On 02/21/2013 04:43 PM, Ryan C. Thompson wrote:
> Ok, so it looks like this splice graph functionality is currently in
> limbo. If I wanted to use it right now with the current release of BioC,
> could I just use the old spliceGraph function from the previous
> GenomicFeatures version? I figure I could get it working by taking the R
> files from the old version, prefixing a few things with
> "GenomicFeatures::", and then sourcing the files.

it would be better to download and install from svn, for your version of R, 
e.g., for Bioc 2.11 / R-2.15.2

  svn co 
https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/SpliceGraph
   R CMD INSTALL SpliceGraph

Martin

>
>
> On 02/21/2013 03:05 PM, Tim Triche, Jr. wrote:
>> yes, that
>>
>>
>> On Thu, Feb 21, 2013 at 2:55 PM, Steve Lianoglou
>> <mailinglist.honeypot at gmail.com
>> <mailto:mailinglist.honeypot at gmail.com>> wrote:
>>
>>      On Thu, Feb 21, 2013 at 5:42 PM, Tim Triche, Jr.
>>      <tim.triche at gmail.com <mailto:tim.triche at gmail.com>> wrote:
>>      > the SpliceGraph and SpliceGrapher packages took over that
>>      functionality
>>
>>      Which are presumably only available via svn at the moment?
>>
>>      I see that SpliceGraph is in svn and not on the devel package list --
>>      I can't find SplieGrapher anywhere, tho.
>>
>>      Maybe you mean SplicingGraphs?
>>
>>      -steve
>>
>>      --
>>      Steve Lianoglou
>>      Graduate Student: Computational Systems Biology
>>       | Memorial Sloan-Kettering Cancer Center
>>       | Weill Medical College of Cornell University
>>      Contact Info: http://cbio.mskcc.org/~lianos/contact
>>      <http://cbio.mskcc.org/%7Elianos/contact>
>>
>>
>>
>>
>> --
>> /A model is a lie that helps you see the truth./
>> /
>> /
>> Howard Skipper
>> <http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>
>
>
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