I think is not an
option for BioC/Rbowtie.
I hope that resolves also the issue on El Capitan.
Michael
On 19.04.2017 13:47, Martin Morgan wrote:
> On 04/19/2017 05:45 AM, Michael Stadler wrote:
>> Dear BioC core,
>>
>> Thanks for the report, Herve. If I understand correctly,
something to worry about?
I hope to get back with a solution for the bowtie issue soon.
Michael
On 19.04.2017 13:47, Martin Morgan wrote:
> On 04/19/2017 05:45 AM, Michael Stadler wrote:
>> Dear BioC core,
>>
>> Thanks for the report, Herve. If I understand correctl
Dear BioC core,
Thanks for the report, Herve. If I understand correctly, there is
nothing I can do at this point to make QuasR green on windows, correct?
I have another question regarding QuasR not building on veracruz2: The
vignette does not build currently, reporting:
Error on
Dear Jurat,
Maybe this would be better asked on support.bioconductor.org.
I don't think I fully understand what you intend to do (a fully working
example would help), but here are two ideas that could be useful:
1. Maybe a single findOverlaps() will be enough to find all you need:
D <-
for the report. I'll look into this.
H.
On 04/22/2014 08:29 AM, Michael Stadler wrote:
Dear Herve,
We are hitting a 'memory not mapped' problem when using trimLRpatterns
as detailed below. I did not manage to reproduce it with few sequences,
so I have to refer to a publicly available sequence
(based on bowtie 1.0.1)
- OS X 10.9 onwards and everything else uses Rbowtie = 1.4.5
(based on bowtie 1.0.1 /patched bugs-312).
Thanks again for your efforts,
Michael
On 14.06.2014 01:31, Dan Tenenbaum wrote:
Hi Michael,
- Original Message -
From: Michael Stadler
Hi Dan,
I'm cc'ing the list; maybe somebody else has experienced differences
between petty and perceval.
Rbowtie release (1.4.5) is not building under OS X 10.6.8 (petty).
Rbowtie release (1.4.5) and development (1.5.5) are virtually identical
(only DESCRIPTION and NEWS differ).
The
you changed
in between?
Best,
Kasper
On Fri, Jun 13, 2014 at 3:32 AM, Michael Stadler michael.stad...@fmi.ch
mailto:michael.stad...@fmi.ch wrote:
Hi Dan,
I'm cc'ing the list; maybe somebody else has experienced differences
between petty and perceval.
Rbowtie
available before tomorrow though.
But, again, this new version (1.25.18) is similar to the current
version (1.25.17), so you can re-install now with
biocLite(AnnotationDbi). No need to wait until tomorrow.
HTH,
H.
On 04/09/2014 12:23 AM, Michael Stadler wrote:
Dear Bioc gurus,
Since a few
Dear Bioc gurus,
Since a few days, QuasR devel (1.3.13 and 1.3.14) is failing on some
unit tests, which turns out to be reproducible independent of QuasR and
might be related to R getting the wrong method for [[-.
The following works fine...
library(GenomicRanges)
grl -
I agree that the profile or metagene plot is useful and widely applied.
Creating such a plot consists of several steps, including:
- quantifying and accumulating signal around sites of interest
- normalization
- visualization
The qProfile() function in QuasR was designed to do the
(release) and 1.5.44 (devel).
Valerie
On 03/07/13 05:43, Michael Stadler wrote:
Here is the second attachment (variants.vcf) that was missing from the
first message.
Michael
On 03/07/2013 02:40 PM, Michael Stadler wrote:
Dear Valerie and colleagues,
I have recently started using
Dear Valerie and colleagues,
I have recently started using the VariantAnnotation package, which is a
huge asset for much of my work with sequence variants - thank you!
I have a question regarding the following example (it makes use of two
small text files, annot.gtf and variants.vcf, attached to
Here is the second attachment (variants.vcf) that was missing from the
first message.
Michael
On 03/07/2013 02:40 PM, Michael Stadler wrote:
Dear Valerie and colleagues,
I have recently started using the VariantAnnotation package, which is a
huge asset for much of my work with sequence
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