Tim Triche, Jr. | 5 Jan 01:37 2013
Picon

Re: status of visnab

A shiny version of visnab would be insanely great. Might be possible to farm out at least some of the heavy
lifting for eg Circos style plots to d3, which is also insanely great. 

Off topic, but have you played with Scribl at all?  It seemed fairly usable for some of the tasks I find IGV
handles. 

I can't say I will miss IGV if something better (webbier) comes along, but it is extensible in some important
respects. The extending does take some work, though, and Java would not be my first choice for writing
extensions if R and/or JS alternatives are available. 

--t

On Jan 4, 2013, at 3:58 PM, Michael Lawrence <lawrence.michael@...> wrote:

> The visnab package has different goals from IGV. It aims to provide an extensible, R-based platform for
interactive genomic visualization. Currently, IGV isn't very extensible at all, i.e., no plugin
support, some nice scripting capabilities via its HTTP interface but no callback handling.  We decided to
focus our energy on ggbio for a while, but Tengfei is still very much interested in pushing visnab forward.
It is currently implemented on top of the R/Qt interface. One idea that has been floated is a port to the web
browser, while retaining R callback support, via something like shiny. Over the holidays, I started
porting the qtpaint API to javascript and the HTML5 canvas. So the foundations are forming.
> 
> Michael
> 
> 
> 
> On Fri, Jan 4, 2013 at 3:17 PM, Tim Triche, Jr. <tim.triche@...> wrote:
>> IGV would seem to have obsoleted some aspects of visnab.
>> 
>> ggbio, on the other hand, is awesome, as is Gviz.  Perhaps those may meet
>> your needs?  Tengfei has certainly been pouring effort into ggbio, and Gviz
>> is also released.  the two are complementary IMHO
>> 
>> 
>> 
>> 
>> On Fri, Jan 4, 2013 at 2:41 PM, Dan Tenenbaum <dtenenba@...> wrote:
>> 
>> > Hi Abhishek,
>> >
>> > On Fri, Jan 4, 2013 at 2:32 PM, Abhishek Pratap <apratap@...> wrote:
>> > > I saw an old note to myself that I wrote a while ago to check on
>> > > visnab...and I dont see it as part of bioC as of now. Can anyone who is
>> > > aware of the developments give me an update on the status of the
>> > package. I
>> > > am interested in playing with it.
>> >
>> > According to this github page:
>> >
>> > https://github.com/tengfei/visnab/wiki/Installation-Instruction
>> >
>> > visnab is not released to BioC yet.
>> >
>> > Perhaps Tengfei can give us a further status update.
>> >
>> > Dan
>> >
>> >
>> >
>> >
>> > >
>> > > Thanks!
>> > > -Abhi
>> > >
>> > >         [[alternative HTML version deleted]]
>> > >
>> > > _______________________________________________
>> > > Bioconductor mailing list
>> > > Bioconductor@...
>> > > https://stat.ethz.ch/mailman/listinfo/bioconductor
>> > > Search the archives:
>> > http://news.gmane.org/gmane.science.biology.informatics.conductor
>> >
>> > _______________________________________________
>> > Bioconductor mailing list
>> > Bioconductor@...
>> > https://stat.ethz.ch/mailman/listinfo/bioconductor
>> > Search the archives:
>> > http://news.gmane.org/gmane.science.biology.informatics.conductor
>> >
>> 
>> 
>> 
>> --
>> *A model is a lie that helps you see the truth.*
>> *
>> *
>> Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>
>> 
>>         [[alternative HTML version deleted]]
>> 
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@...
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> 

	[[alternative HTML version deleted]]

_______________________________________________
Bioconductor mailing list
Bioconductor@...
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


Gmane