On Mon, Oct 13, 2014 at 9:44 PM, Hervé Pagès wrote:
> Hi,
>
> On 10/11/2014 02:25 PM, Vincent Carey wrote:
>
>> On Sat, Oct 11, 2014 at 5:17 PM, Michael Lawrence <
>> lawrence.mich...@gene.com
>>
>>> wrote:
>>>
>>
>> But what it would do exactly?
>>>
>>> Probably would want to be able to extract
Hi,
On 10/11/2014 02:25 PM, Vincent Carey wrote:
On Sat, Oct 11, 2014 at 5:17 PM, Michael Lawrence
wrote:
But what it would do exactly?
Probably would want to be able to extract a gene list from a TxDb, then
extract the desired type of structure from the TxDb.
Not too bad right now, but it
Dear Bioconductor-community,
I would like to introduce a new package to you: PAA.
PAA (Protein Array Analyzer) is a package for protein microarray data
analysis (esp., ProtoArray data). PAA imports single color protein
microarray data that has been saved in gpr file format. After pre-proces
Hi Tiphaine,
On 10/13/2014 04:31 PM, Martin, Tiphaine wrote:
Hi,
I wrote a list of functions used in my package called coMET. I decided with my
colleagues to try to publish it in Bioconductor. Currently, it has not been yet
submitted to bioconductor because I would like to be sure that it sa
Hi,
I wrote a list of functions used in my package called coMET. I decided with my
colleagues to try to publish it in Bioconductor. Currently, it has not been yet
submitted to bioconductor because I would like to be sure that it satisfies all
your guidelines.
A list of functions is useful only
The BioC 3.0 branch is now ready.
Remember, you always have access to 2 versions of your package:
the "release" and the "devel" versions.
Right now the "release" version of your package (which is not
officially released yet but will be on Tuesday if
everything goes well) is in the 3.0 branch and
It would be nice to know the use case of the internal keyword here. I've
use it to avoid listing functions in the index (RGtk2 has thousands of
functions). But in general, it's not a good idea to be exporting things
that are truly internal. Perhaps internal methods on exported generics, but
even th
Hello BioC developers,
We will be creating the Bioconductor 3.0 branch today at 2:30 PM
Seattle time. (21:30 UTC). This is about an hour from now.
Please stop all commits to trunk before 2:30PM and do not resume until
further notice.
We will send another email when it is OK to resume commits. Th
- Original Message -
> From: "Tiphaine Martin"
> To: bioc-devel@r-project.org
> Sent: Monday, October 13, 2014 1:29:08 PM
> Subject: [Bioc-devel] runnable examples for internal function ?
>
> Hi,
>
>
> I would like to know if I need to add a runnable example for each
> function that h
Hi,
I would like to know if I need to add a runnable example for each function that
has keyword either internal or not.
I ask that because with BiocCheck, version 1.0.2, I had a message for function
with keyword "internal" such as "
Checking exported objects have runnable examples...
* C
On 10/13/2014 07:45 AM, Michael Lawrence wrote:
But the behavior has changed for this case:
merge(Seqinfo("chr1"), Seqinfo())
Before it was "each has seqlevels not in the other" but now it is "these
two sets are disjoint". Subtle difference, but I think it's important?
What has changed is tha
But the behavior has changed for this case:
merge(Seqinfo("chr1"), Seqinfo())
Before it was "each has seqlevels not in the other" but now it is "these
two sets are disjoint". Subtle difference, but I think it's important?
On Sun, Oct 12, 2014 at 11:46 PM, Hervé Pagès wrote:
> Hi Michael,
>
>
both methods work well.
Thanks,
Tiphaine
From: Hahne, Florian
Sent: 13 October 2014 08:46
To: Vincent Carey; Martin, Tiphaine
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Non-ASCII in datase from Biomart EMBL via Gviz package
Hi Tiphaine,
You c
Hi Tiphaine,
You can follow Vince¹s advice and transform all the data into proper ASCII
character. Or you can just get rid of the culprit (being the @biomart slot
of the object) before serialising. The easiest way to do that is:
foo@biomart <- NULL
The slot is only present to cache the BiomaRt conn
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