Hi,
TL;DR: what do you use to manage workflows and pipelines for you research? Knitr
or similar? Galaxy? Taverna?
Long version:
in my lab we are thinking about restyling our pipeline management
system and would like to exploit as much as possible the wealth of
annotations available in the Annota
On Mon, Jun 20, 2016 at 11:36 AM, Sean Davis wrote:
> Hi, Elena.
>
> What do your pipelines need to do?
The idea behind our system is to be as general as possible. We are
mainly interested in human genomic/transcriptomic...we stem from
standard differential expression analyses
on microarray/RNAse
I think this is a recent break. I'm mostly concerned because I need to
use this "broken" functionality in a tutorial for BioC2016 this week
and it would require changes to package internals, not the vignette,
in order to fix this at my end.
library(SummarizedExperiment)
se <- SummarizedExperiment(
Hi Pete,
Because of various issues with the builds, some recent changes to
some core packages have not been able to propagate. So for example
the version of GenomicRanges currently available via biocLite() is
1.25.4, which is lagging behind the version that is in svn (1.25.8).
I think this could
I was going to say that for the tutorial users it might be easier to
use devtools::install_github('Bioconductor-mirror/GenomicRanges')
rather than svn.
However, from
https://github.com/Bioconductor-mirror/GenomicRanges/blob/master/DESCRIPTION#L13
you can see that it's outdated.
On Mon, Jun 20, 2
On 06/20/2016 09:22 PM, Leonardo Collado Torres wrote:
I was going to say that for the tutorial users it might be easier to
use devtools::install_github('Bioconductor-mirror/GenomicRanges')
FWIW biocLite("Bioconductor-mirror/GenomicRanges") invokes
install_github(). Martin
rather than svn.
