On 04/08/2016 02:34 PM, Obenchain, Valerie wrote:
> Hi,
>
> It sounds like we have agreement on these points:
>
> - Add support for sequences
> - Keep the OrganismDb name
> - Do provide pre-built packages
>
> I'm not sure we got much weigh in on the package name. I tend towards a
> more descriptive
Hi,
It sounds like we have agreement on these points:
- Add support for sequences
- Keep the OrganismDb name
- Do provide pre-built packages
I'm not sure we got much weigh in on the package name. I tend towards a
more descriptive name. This post (to me) is an example of the confusion
that can co
Dear Valerie,
Thank you for the update.
1) Class name: I'd definitely prefer the exisiting naming over the three
other suggestions you gave.
2) Pre-made packages: Yes, I think it would be great to have such packages
available for well-established Bioc model organisms, i.e. as returned by
Annotat
My only concern regarding AnnotationHub is offline use. I find that I'm more
productive if I turn off the network interface altogether... Maybe I'm the only
one. BiomaRt also scarred me a little.
--t
> On Apr 7, 2016, at 8:34 AM, Vincent Carey wrote:
>
>
>
>> On Thu, Apr 7, 2016 at 11:24 A
On Thu, Apr 7, 2016 at 11:24 AM, Tim Triche, Jr.
wrote:
> Great! This is an awesome opportunity to move to ENSEMBL as a default ;-)
> (only half kidding, by the way)
>
> 1) BSGenome/2bit would be great -- I use this sometimes to generate fusion
> transcripts with defined breakpoints to supplemen
Great! This is an awesome opportunity to move to ENSEMBL as a default ;-)
(only half kidding, by the way)
1) BSGenome/2bit would be great -- I use this sometimes to generate fusion
transcripts with defined breakpoints to supplement existing txomes
2) class name: don't change it
3) pre made pa
On Thu, Apr 7, 2016 at 10:34 AM, Obenchain, Valerie <
valerie.obench...@roswellpark.org> wrote:
> BioC developers,
>
> After the release we plan to continue development the OrganismDb class
> and packages. This email outlines some ideas for future direction. We're
> interested in feedback on these
