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,
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
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
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
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
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
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,
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
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
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
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
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