On 04/09/2015 05:57 AM, Ludwig Geistlinger wrote:
Here you go ...
sessionInfo()
R Under development (unstable) (2015-03-09 r67969)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.U
I am happy to announce that our CopywriteR tool is now available on the
development branch of Bioconductor. CopywriteR extracts copy number information
from targeted sequencing using off-target reads (for more information, see
Kuilman et al, Genome Biology 16:49, 2015). This new method allows co
Hi,
I just started to toy around with the new BioC dockers out of curiosity.
As I pulled down the release_core image (running boot2docker under OS X
Yosemite)
docker run -ti bioconductor/release_core R
and then executed
> library(AnnotationHub)
> hub <- AnnotationHub()
I received the following
Hi,
On Thu, Apr 9, 2015 at 10:27 AM, Ludwig Geistlinger
wrote:
> Error in file(con, "r") : cannot open the connection
> In addition: Warning message:
> In file(con, "r") : unable to resolve 'annotationhub.bioconductor.org'
That's strange, on linux it's working. Seems related to network
unavaila
From Aaron Lun.
On a related note, there's now a number of packages involved in
analyzing Hi-C data, e.g., GoTHiC, HiTC, GenomicInteractions and
diffHic. Would it be worth adding a BiocViews term for the Hi-C assay
(maybe under Technology -> Sequencing)?
Cheers,
Aaron
--
Aaron Lun
PhD student
Dear Elena,
thank you for your quick response.
Seems as I have make this up to early - it works now for me as well, must
have been a pure connection issue.
Thx for pointing me to the docker scripts (I must have overread it, is ac
tually also stated under http://bioconductor.org/help/docker/).
So
Here you go ...
> sessionInfo()
R Under development (unstable) (2015-03-09 r67969)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en
Hello to those working with flow cytometry data,
we are excited to announce that our package, FlowRepositoryR, is now
available in BioConductor (devel). This package provides a light interface
to access FlowRepository (https://flowrepository.org/) data from within R.
FlowRepository is a public repo
Hi,
Just a reminder that according to the release schedule
(http://bioconductor.org/developers/release-schedule/#april-9) we will be
disabling commits to the current release (3.0) branch today at 4:20PM Seattle
time and then running one last build for that branch.
Also, another reminder to pl
Hi,
As I pulled down the devel_core image (running boot2docker under OS X
Yosemite)
docker run -ti bioconductor/release_core R
and then executed
> library(AnnotationHub)
> hub <- AnnotationHub()
and selected the recently integrated GSE62944 TCGA dataset (announced in
the latest BioC newsletter
Please provide sessionInfo()
The class is defined in AnnotationHub in devel. Perhaps it is not suitably
exported.
On Thu, Apr 9, 2015 at 5:33 AM, Ludwig Geistlinger <
ludwig.geistlin...@bio.ifi.lmu.de> wrote:
> Hi,
>
> As I pulled down the devel_core image (running boot2docker under OS X
> Yose
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