Are there any plans for an online interface to https://git.bioconductor.org/?
I've recently looked into solutions for an open-source in-house
"GitHub/GitLab"-ish, and I've found https://gitea.io/ to be really
nice. It is very easy to install. It has support for various common
user authentication
On 10/25/2017 11:18 AM, Henrik Bengtsson wrote:
I lean to agree with Yaoyong, because I find it helpful to specify (or read):
Depends: R (>= 3.0.0)
which sends a message that "the code is relying on features in R that
was not available prior to R 3.0.0". Also, if that's the only
dependency y
I lean to agree with Yaoyong, because I find it helpful to specify (or read):
Depends: R (>= 3.0.0)
which sends a message that "the code is relying on features in R that
was not available prior to R 3.0.0". Also, if that's the only
dependency you have, then if it passed R CMD check on R 3.0.0 in
What about some more hardware to improve throughput? I think complicating
the test
driving software is less desirable -- although perhaps it is just a day of
week check somewhere.
I can imagine that it fails on wednesday but then passes on thursday and
developer ignores the event...
The failure ha
Emphatic +1
--t
> On Oct 25, 2017, at 9:56 AM, Kasper Daniel Hansen
> wrote:
>
> I think we need to think about this in the long term. Can we add support
> for these major tests in the build system, perhaps not every day, but every
> week or month? The alternative, that it is up to the develo
I think we need to think about this in the long term. Can we add support
for these major tests in the build system, perhaps not every day, but every
week or month? The alternative, that it is up to the developer, is not
great I think. We should still advocate for people writing quicker tests,
but
Model results could be stored in another SE. The contrasts are treated as
samples, and stuff like p-values, effect sizes, etc as assays. Question is
whether those should just be tacked onto a MAE, or kept as separate
objects, or stored along with the MAE in a larger analysis-level workflow
object.
I think analysis of multiassay experiments often will consists of
integration following assay-specific models. Not necessarily, but it will
be a usecase. Organizing multiple model fits together could be useful, for
downstream comparison / integration.
Say you find DMRs and DE genes. Now you want t
hi Hervé,
thanks for your answer, i also think it isn't clear how one would
automatically combine the object-wise metadata, specially if there were
metadata entries with the same name. just wanted to make sure that this
is a design decision and will remain this way in the future.
best regard
Hi Robert,
The object-wise metadata doesn't follow any convention and is typically
used to keep track of things like the file the object is coming from
(if any), the date/time it was created, by who, the call that was used
to create it, plus any other relevant information about the object.
It's
Looks like BiocCodeTools should start checking whether people are using
that and at least make a NOTE of it.
On Tue, Oct 24, 2017 at 8:17 PM, Peter Hickey
wrote:
> A partial answer if you are using the 'testthat' framework: you can use
> `testthat::skip_on_bioc()` to specify that a test should b
hi,
i've the following question on how 'S4Vectors::cbind()' works on
'DataFrame' objects.
let's say i have the following two toy 'DataFrame' objects, each of them
including some elementwise and non-elementwise metadata (i hope i'm
using the right terminology!):
library(S4Vectors)
dtf1 <-
That's great help, Levi, I will try your suggestions.
thank you,
francesco
Il 25/10/2017 00:28, Levi Waldron ha scritto:
OK, I think I'm understanding better now. The best immediate solution that
I can think of is a SummarizedExperiment for each signatures database, then
pasting those Summarize
On 10/25/2017 02:05 AM, Stian Lågstad wrote:
Thank you Martin. Are the core packages being kept as Github mirrors?
yes the core packages are maintained as github mirrors. Martin
On Wed, Oct 25, 2017 at 3:21 AM, Martin Morgan
mailto:martin.mor...@roswellpark.org>>
wrote:
On 10/24/2017
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