Hi Caleb,
Hopefully Herve will chime in regarding SummarizedExperiment, but yes, I
think you can and should inherit from that. The `assays` slot must be an
object of type `Assays`, but that does appear to include a sparse Matrix.
See the comments at the top of Assays-class.R in the tarball for
Hi Caleb,
Per your question on sparse on-disk matrices: is your experimental data coming
in some pre-defined text or binary file format, or are you looking to convert
to a new, custom format to take advantage of the sparsity?
I need to start working on an on-disk sparse matrix implementation
Hi everyone—
I’m working with a team that’s generating single cell ATAC data in large
amounts and am designing the framework of an S4 object to facilitate analyses
in R. I have a couple of high-level questions that I wanted to pose early to
hopefully attain some community guidance in the
On 09/23/2016 12:15 PM, Martin Morgan wrote:
Bioc Developers!
biocViews are an important way for users to navigate to your package.
The following packages have incorrect biocViews terms. To update terms
in your package, visit
http://bioconductor.org/packages/devel/BiocViews.html#___Software
Bioc Developers!
biocViews are an important way for users to navigate to your package.
The following packages have incorrect biocViews terms. To update terms
in your package, visit
http://bioconductor.org/packages/devel/BiocViews.html#___Software
check the 'Develoeprs: check this box...'
Hi Yu,
On 09/23/2016 06:57 AM, Yu Kong wrote:
Hi Hervé,
Thank you so much for help. My package uses JAGS thru the rjags package.
Good. Thanks for clarifying. So can you please remove the
SystemRequirements line from the DESCRIPTION file of your
package?
I just installed JAGS on tokay1.
You'll need to either `importFrom(Biobase, only, the, symbols,
needed)` or use the `except="combine"` argument to `import()`.
On Fri, Sep 23, 2016 at 4:59 AM, THEVENOT Etienne 207099
wrote:
> Dear Bioc Team,
>
> First of all thanks a lot again for all the time you spend
In general you can assume this to be the case for core functionality like
the stuff in Biobase.
What you should do however, since combine() is an S4 method, is import the
S4 method from BiocGenerics. In fact, it is a good idea to check which
generics are defined in BiocGenerics and consider
Dear Bioc Team,
First of all thanks a lot again for all the time you spend developing and
maintaining the Bioc repository.
I recently added 'Biobase' as "suggests" in the 'biosigner' package in order to
have the biosign method work on 'ExpressionSet' objects (devel version of
'biosigner').
Yes, that was the strange thing (for me at least): some packages showed
"all" and some showed "some" and a cursory look did not reveal any pattern.
R.
On Fri, 23-09-2016, at 08:26, Hervé Pagès wrote:
> On 09/22/2016 11:09 PM, Ramon Diaz-Uriarte wrote:
>> Hi Hervé,
>>
>>
Hi Yu,
On 09/22/2016 02:15 PM, Yu Kong wrote:
Dear BioConductor community,
My package (MADSEQ) passed the build on Linux (*malbec1*) and Mac (*morelia*)
build servers. However it fails on Windows (tokay1) server for multiple
days. Our package is a Bayesian model depends on JAGS sampler. The
On 09/22/2016 11:09 PM, Ramon Diaz-Uriarte wrote:
Hi Hervé,
Thanks for the clarification; (what I was surprised about was that some say
"some" and others said "all",
Oh really? I went directly to the landing page of your package, saw
the "some", and didn't mind checking other package landing
12 matches
Mail list logo