Thanks. Fixed, the change will propagate soon.
Dan
- Original Message -
> From: "Diego Diez"
> To: "Hervé Pagès"
> Cc: "Dan Tenenbaum" , "bioc-devel"
>
> Sent: Friday, October 16, 2015 5:11:08 PM
> Subject: Re: [Bioc-devel] BioC 3.2 branch created
>
> Nice addition, thank you. Just w
Nice addition, thank you. Just want to note that now the 3.1 page says
"April 17, 2005". Thats a long time ago! I guess it means "April 17,
2015".
Diego
On Sat, Oct 17, 2015 at 3:30 AM, Hervé Pagès wrote:
> On 10/16/2015 10:52 AM, Dan Tenenbaum wrote:
>>
>>
>>
>> - Original Message -
>>>
Thanks Herve and Michael,
I'll just use my linux box.
Sonali.
On 10/16/2015 1:15 PM, Hervé Pagès wrote:
Hi Sonali, Michael,
Tried on Linux and Windows with BioC 3.3 and couldn't reproduce
this either (got the expected/usual warning about the cds cumulative
length not being a multiple of 3).
Hi Sonali, Michael,
Tried on Linux and Windows with BioC 3.3 and couldn't reproduce
this either (got the expected/usual warning about the cds cumulative
length not being a multiple of 3).
BTW I think GenomicRanges is failing in the devel builds because
of some issues with AnnotationHub. I don't
Update , I just see a warning on my linux box ( see the error only on
windows)
> txdb <- makeTxDbFromUCSC(genome = "hg19", tablename = "refGene")
Download the refGene table ... OK
Download the refLink table ... OK
Extract the 'transcripts' data frame ... OK
Extract the 'splicings' data frame ...
Seemed to work for me. Could just be a transient issue with UCSC?
On Fri, Oct 16, 2015 at 12:02 PM, Arora, Sonali wrote:
> Hi ,
>
> I get an error when creating a txdb object for hg19 from the refGene Table
>
>> txdb <- makeTxDbFromUCSC(genome = "hg19", tablename = "refGene")
> Error in tableName
Hi ,
I get an error when creating a txdb object for hg19 from the refGene Table
> txdb <- makeTxDbFromUCSC(genome = "hg19", tablename = "refGene")
Error in tableNames(ucscTableQuery(session, track = track)) :
error in evaluating the argument 'object' in selecting a method for
function 'tableN
On 10/16/2015 10:52 AM, Dan Tenenbaum wrote:
- Original Message -
From: "Hervé Pagès"
To: "Dan Tenenbaum" , "Levi Waldron"
Cc: "bioc-devel"
Sent: Friday, October 16, 2015 10:07:03 AM
Subject: Re: [Bioc-devel] BioC 3.2 branch created
Hi Dan,
Thanks for making that change. Would be
- Original Message -
> From: "Hervé Pagès"
> To: "Dan Tenenbaum" , "Levi Waldron"
>
> Cc: "bioc-devel"
> Sent: Friday, October 16, 2015 10:07:03 AM
> Subject: Re: [Bioc-devel] BioC 3.2 branch created
>
> Hi Dan,
>
> Thanks for making that change. Would be great to have this for the
Hi Dan,
Thanks for making that change. Would be great to have this for the
previous releases too. One often lands on an announcement page directly
from Google and has no easy way to tell when that release happened.
Thanks,
H.
On 10/16/2015 08:45 AM, Dan Tenenbaum wrote:
Done, the change shoul
Sure, "*" makes more sense for strand, given the precedent.
On Fri, Oct 16, 2015 at 9:55 AM, Hervé Pagès wrote:
> On 10/16/2015 09:28 AM, Michael Lawrence wrote:
>>
>> I kind of wish it would return NA for things like seqnames and strand,
>> but yes that would be very useful.
>
>
> Could do this
On 10/16/2015 09:28 AM, Michael Lawrence wrote:
I kind of wish it would return NA for things like seqnames and strand,
but yes that would be very useful.
Could do this for seqnames() but I'm hesitant to do this for strand().
If you look at ?strand in BiocGenerics, ‘*’ is used when the exact
str
I kind of wish it would return NA for things like seqnames and strand,
but yes that would be very useful.
On Fri, Oct 16, 2015 at 9:15 AM, Hervé Pagès wrote:
> Hi Michael, Martin,
>
> On 10/16/2015 06:48 AM, Michael Lawrence wrote:
>>
>> It does seem like starting with the more general data struc
Hi Michael, Martin,
On 10/16/2015 06:48 AM, Michael Lawrence wrote:
It does seem like starting with the more general data structure is the
better approach, but I couldn't find an easy way to move the paired subset
of GAlignmentsList to GAlignmentPairs. You mention a coercion, but it's not
obviou
Done, the change should appear within 20 minutes. Thanks for the suggestion.
Dan
- Original Message -
> From: "Levi Waldron"
> To: "bioc-devel"
> Sent: Friday, October 16, 2015 8:23:17 AM
> Subject: Re: [Bioc-devel] BioC 3.2 branch created
>
> Just a small suggestion, it might be helpf
Just a small suggestion, it might be helpful to put a date on
https://www.bioconductor.org/news/bioc_3_2_release/ - currently it's not
obvious when you land on that page when the announcement was made, or that
this is the current release version.
Thanks core team for your hard work in getting anot
It does seem like starting with the more general data structure is the
better approach, but I couldn't find an easy way to move the paired subset
of GAlignmentsList to GAlignmentPairs. You mention a coercion, but it's not
obvious to me, unfortunately.
Another approach would be a GAlignmentPairs wh
I see, thanks. Was just using an old version (wrong laptop), so missed the
mapqFilter().
On Fri, Oct 16, 2015 at 5:10 AM, Morgan, Martin <
martin.mor...@roswellpark.org> wrote:
>
>
> > -Original Message-
> > From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf Of
> > Micha
> -Original Message-
> From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf Of
> Michael Lawrence
> Sent: Friday, October 16, 2015 7:41 AM
> To: bioc-devel@r-project.org
> Subject: [Bioc-devel] readGAlignmentPairs with discordant strand
>
> Now that GAlignmentPairs suppor
> -Original Message-
> From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf Of
> Michael Lawrence
> Sent: Friday, October 16, 2015 7:56 AM
> To: bioc-devel@r-project.org
> Subject: [Bioc-devel] ideas for ScanBamParam filters
>
> Maybe I just missed these, but these are a
Maybe I just missed these, but these are a couple of things we could filter
by, in addition to what's there already:
- Minimum MAPQ
- Read group
The first is mostly for convenience, but the second should also benefit
performance.
I can help implement this, but wanted to make sure this is a reaso
Now that GAlignmentPairs supports discordant strand between mates, how hard
would it be to relax that restriction on readGAlignmentPairs()?
Also, would be nice if getDumpedAlignments() returned those dumped by
readGAlignmentPairs(). Right now, I'm reading a GAlignments (with the extra
mcols) and c
Dear All,
I can confirm that the issue is fixed in the latest BioC / R versions.
Thanks a lot.
Yours,
Marcin
On Fri, Oct 16, 2015 at 7:09 AM, Michael Lawrence wrote:
> On Thu, Oct 15, 2015 at 11:04 PM, Hervé Pagès
> wrote:
>
> > Hi Michael,
> >
> > On 10/15/2015 10:08 AM, Michael Lawrenc
On Thu, Oct 15, 2015 at 11:04 PM, Hervé Pagès wrote:
> Hi Michael,
>
> On 10/15/2015 10:08 AM, Michael Lawrence wrote:
>
>> Tangentially related, it seems like nchar is worth defining in
>> BiocGenerics, with a signature of "x". I saw that Biostrings uses "type",
>> but I'm not sure why.
>>
>
> T
Dear Bioconductor developers,
As the Bioconductor was released, I would like to present two new
packages : DAPAR and Prostar.
DAPAR (Differential Analysis for Proteomics Analysis with R) is an R
package for the analysis mass spectrometry-based discovery proteomics
quantitative dataset. It is
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