On 03/16/2015 05:31 PM, Hervé Pagès wrote:
On 03/16/2015 04:06 PM, Michael Lawrence wrote:
On Mon, Mar 16, 2015 at 3:12 PM, Robert Castelo mailto:robert.cast...@upf.edu>> wrote:
+1 IMO BioC could adopt the zero-width ranges representation for
insertions, adapting readVcf(), writeVcf()
- Original Message -
> From: "Kasper Daniel Hansen"
> To: "Tiphaine Martin"
> Cc: "Dan Tenenbaum" , "bioc-devel"
>
> Sent: Monday, March 16, 2015 6:43:40 PM
> Subject: Re: [Bioc-devel] Bioconductor 3.1 release schedule now available
>
>
> If your package passes build and check witho
If your package passes build and check without warnings it happens
automatically, including the version bump.
If this is the first release of your package, it should have a version
number of 0.99.Z (which seems to be the case). This is checked / fixed
when your package gets accepted.
Best,
Kaspe
Dear Dan,
I have 2 naive questions.
I would like to know whether we (developers of a R package currently only in
the development version of Bioconductor) need to say that we would like to have
our packages accessible in the next version of Bioconductor or it is automatic
for any packages passin
- Original Message -
> From: "Levi Waldron"
> To: bioc-devel@r-project.org
> Sent: Monday, March 16, 2015 11:30:54 AM
> Subject: [Bioc-devel] developer profiles on bioconductor.org
>
> Since our Seattle team is always looking for extra work (!), I was
> thinking
> it would be nice to in
On 03/16/2015 04:06 PM, Michael Lawrence wrote:
On Mon, Mar 16, 2015 at 3:12 PM, Robert Castelo mailto:robert.cast...@upf.edu>> wrote:
+1 IMO BioC could adopt the zero-width ranges representation for
insertions, adapting readVcf(), writeVcf(), XtraSNPlocs.*, etc., to
deal with each
On Mon, Mar 16, 2015 at 3:12 PM, Robert Castelo
wrote:
> +1 IMO BioC could adopt the zero-width ranges representation for
> insertions, adapting readVcf(), writeVcf(), XtraSNPlocs.*, etc., to deal
> with each corresponding beast, be VCF, dbSNP or the like. Who knows, VCF
> could also change thei
Using a GAlignments object to show 3 different representations of the
same insertion (three nucleotides (TTT) inserted between positions 10
and 11):
library(GenomicAlignments)
gal <- GAlignments(Rle("chr1", 3), pos=c(10L, 10L, 11L),
cigar=c("1M3I1M", "1M3I", "3I"),
+1 IMO BioC could adopt the zero-width ranges representation for
insertions, adapting readVcf(), writeVcf(), XtraSNPlocs.*, etc., to deal
with each corresponding beast, be VCF, dbSNP or the like. Who knows, VCF
could also change their representation in the future and it'll be a
headache to upda
Hi Laurent,
On 03/10/2015 07:28 AM, Laurent Gatto wrote:
Dear all,
Two possible candidates for BiocGenerics:
GenomeInfoDb::species
standardGeneric for "species" defined from package "GenomeInfoDb"
function (x)
standardGeneric("species")
Methods may be defined for arguments: x
Use showMet
There would be a LOT of value in having core packages use exactly the same
representation; I don't have any opinion about which one is best.
Kasper
On Mon, Mar 16, 2015 at 3:38 PM, Hervé Pagès wrote:
> On 03/16/2015 09:22 AM, Michael Lawrence wrote:
>
>> Yes, I think it would make sense for the
On 03/16/2015 09:22 AM, Michael Lawrence wrote:
Yes, I think it would make sense for the Xtra package to follow the
established convention in VariantAnnotation/VCF.
I don't know. I agree it would be nice to use a more consistent
representation of insertions across the software but I'm not convi
Since our Seattle team is always looking for extra work (!), I was thinking
it would be nice to integrate developer profiles on support.bioconductor.org
to the packages they maintain. E.g. links to their packages, stats for
those packages, feeds for recent updates to those packages and aggregated
b
- Original Message -
> From: "Steven Barrett"
> To: bioc-devel@r-project.org
> Sent: Monday, March 16, 2015 8:54:58 AM
> Subject: [Bioc-devel] No vignette contents page/fig refs with Devtools build
>
> Hello,
>
> I have a problem with the automated vignette construction during a
> devt
Dear Steven,
thank you for your inquiry. It would be helpful if you could provide more
details regarding your issue. In particular, a minimal example reproducing
the problem would be a great starting point.
Cheers,
Andrzej
On Mon, Mar 16, 2015 at 4:54 PM, Steven Barrett
wrote:
> Hello,
>
> I h
Yes, I think it would make sense for the Xtra package to follow the
established convention in VariantAnnotation/VCF.
On Mon, Mar 16, 2015 at 9:16 AM, Robert Castelo
wrote:
> dear devel people, specially Val and Michael,
>
> Hervé has recently added an annotation package that includes non-SNVs
>
dear devel people, specially Val and Michael,
Hervé has recently added an annotation package that includes non-SNVs
variants from dbSNP, it is called:
library(XtraSNPlocs.Hsapiens.dbSNP141.GRCh38)
if you execute the corresponding example you'll see the kind of
information stored in the packa
Hello,
I have a problem with the automated vignette construction during a devtools
build.
The vignette is encoded in an .rnw file and I'm using Knitr.
When I compile the .rnw in RStudio it yields a .pdf with the contents page and
figure label references properly instantiated.
However, when I
Hej Valerie!
Yes, it did fix the issue, but only after I also installed the snow package.
Could it be that that's another dependency that has been overlooked in
BiocParallel?
Nico
---
Nicolas Delhomme
The Street Lab
Department of Pl
Hi Nico,
Can you try again with BiocParallel 1.1.16? Likely related to this post,
https://stat.ethz.ch/pipermail/bioc-devel/2015-March/007114.html
Valerie
On 03/16/2015 07:05 AM, Nicolas Delhomme wrote:
Hej!
Martin I guess that's for you :-) And I suppose it might only be temporary (due
t
Hej!
Martin I guess that's for you :-) And I suppose it might only be temporary (due
to development in BIocParallel/ShortRead), but I stumbled on the following:
library(ShortRead)
srdistance(DNAStringSet("AA"),"AAATAA")
fails with the following error:
Error in bplapply(X, FUN, ..., BPRESUM
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