Re: [Bioc-devel] exptData(SummarizedExperiment)

On Wed, May 13, 2015 at 1:48 PM, Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: > the original workflow idea was exactly that it should go beyond a single > package. > My question here was not about workflow intent. It was about the vehicle for maintaining a workflow. Some are crea

Re: [Bioc-devel] exptData(SummarizedExperiment)

I personally don't care as long as I have a cubbyhole for unstructured data and the name of that cubbyhole doesn't change every few weeks hence the patch that I sent about 12 hours after complaining :-) Statistics is the grammar of science. Karl Pearson

Re: [Bioc-devel] exptData(SummarizedExperiment)

the original workflow idea was exactly that it should go beyond a single package. Having domain specific cores might be controversial since we often have multiple packages competing in the same domain. To some extent the GenomicRanges/Biostring/etc/etc is a special case of this, where "everyone"

Re: [Bioc-devel] exptData(SummarizedExperiment)

Agreed that the workflow vehicle should get more attention. Do all workflows correspond to packages? On Tue, May 12, 2015 at 7:31 PM, Michael Lawrence wrote: > I like the idea of having multiple, domain-specific cores. Those could also > serve as a vehicle for high-level documentation, includin

Re: [Bioc-devel] exptData(SummarizedExperiment)

I like the idea of having multiple, domain-specific cores. Those could also serve as a vehicle for high-level documentation, including the workflows but also more "cheat-sheet" and/or cookbook-style documentation. Rafa has brought this up on the phone calls. On Tue, May 12, 2015 at 4:10 PM, Hervé

Re: [Bioc-devel] exptData(SummarizedExperiment)

SummarizedExperiment was just an example. I agree it can be a little challenging for end users to know where to find a particular functionality but I'm not sure about using "meta" packages to address that. At least I feel we should probably avoid creating new "meta" packages out of the blue, with

Re: [Bioc-devel] exptData(SummarizedExperiment)

It's more general than SummarizedExperiment. I think people would appreciate a simple way to load the core, without having to remember, for example, that VCF reading is in VariantAnnotation. On Mon, May 11, 2015 at 9:51 PM, Hervé Pagès wrote: > Hi Michael, > > On 05/11/2015 05:35 PM, Michael Law

Re: [Bioc-devel] exptData(SummarizedExperiment)

Hi Michael, On 05/11/2015 05:35 PM, Michael Lawrence wrote: Splitting stuff into different packages is good for modularity, but tough on the mind of the user. What about having some sort of "meta" package that simply loads the core infrastructure packages? Named something simple like "Genomics"

Re: [Bioc-devel] exptData(SummarizedExperiment)

I'll write a patch... I'd have to anyway :-) --t > On May 11, 2015, at 5:10 PM, Hervé Pagès wrote: > > Hi Tim, > > The SummarizedExperiment class is being replaced with the > RangedSummarizedExperiment class from the new SummarizedExperiment > package. This is a work-in-progress and the name a

Re: [Bioc-devel] exptData(SummarizedExperiment)

Splitting stuff into different packages is good for modularity, but tough on the mind of the user. What about having some sort of "meta" package that simply loads the core infrastructure packages? Named something simple like "Genomics" or "GenomicsCore". On Mon, May 11, 2015 at 5:10 PM, Hervé Pagè

Re: [Bioc-devel] exptData(SummarizedExperiment)

Hi Tim, The SummarizedExperiment class is being replaced with the RangedSummarizedExperiment class from the new SummarizedExperiment package. This is a work-in-progress and the name and internal representation of the RangedSummarizedExperiment class are not finalized yet. The main goal for now is