Re: [Bioc-devel] any interest in a BiocMatrix core package?

A belated follow-up on this thread. I've created a minimal package and GitHub repo at https://github.com/Bioconductor/MatrixGenerics; might I suggest we move the discussion there for the time being? I've created some issues already to discuss the main points. These would really benefit from

Re: [Bioc-devel] any interest in a BiocMatrix core package?

On 11/02/2017 06:20 PM, Peter Hickey wrote: As Michael notes, I think the scope here is broader than considering S4 generics for functions in base R. To summarise, I think we would be looking to have S4 generics for the following: - All(?) the row*/col* functions in matrixStats (NB: matrixStats

Re: [Bioc-devel] any interest in a BiocMatrix core package?

> Martin Morgan > on Thu, 2 Nov 2017 06:17:19 -0400 writes: > On 11/02/2017 05:00 AM, Martin Maechler wrote: >>> "ML" == Michael Lawrence >>> on Wed, 1 Nov 2017 14:13:54 -0700 writes: >> >> >

Re: [Bioc-devel] any interest in a BiocMatrix core package?

On 11/02/2017 05:00 AM, Martin Maechler wrote: "ML" == Michael Lawrence on Wed, 1 Nov 2017 14:13:54 -0700 writes: > Probably way easier to add the generics to the Matrix > package and everyone just depends on that. Yes! It is 'Recommended' and comes

Re: [Bioc-devel] any interest in a BiocMatrix core package?

> "ML" == Michael Lawrence > on Wed, 1 Nov 2017 14:13:54 -0700 writes: > Probably way easier to add the generics to the Matrix > package and everyone just depends on that. Yes! It is 'Recommended' and comes with every R installation, and has had

Re: [Bioc-devel] any interest in a BiocMatrix core package?

..@gmail.com>>> Sent: Saturday, 25 February 2017 8:34:58 AM To: Aaron Lun Cc: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>> Subject: Re: [Bioc-devel] any interest in a BiocMatrix core package

Re: [Bioc-devel] any interest in a BiocMatrix core package?

one > could > >>>> contemplate benchmarking with it? > >>>> > >>>> On Fri, Feb 24, 2017 at 7:08 PM, Bemis, Kylie < > k.be...@northeastern.edu< > >>>> mailto:k.be...@northeastern.edu>> > >>>> wrote: > >>&g

Re: [Bioc-devel] any interest in a BiocMatrix core package?

ter/HDF5Array/bigmemory/etc. >>>>> objects at the R level, especially if using a frontend like >>> DelayedArray >>>> on >>>>> top of them, but it would be nice to have a common C++ API that I could >>>>> hook into as well (a la Rcpp),

Re: [Bioc-devel] any interest in a BiocMatrix core package?

>>> On Fri, Feb 24, 2017 at 7:08 PM, Bemis, Kylie <k.be...@northeastern.edu >>>> < >>>> mailto:k.be...@northeastern.edu>> >>>> wrote: >>>> >>>> It’s not there yet, but I plan to expose a C++ API for my disk-backed >

Re: [Bioc-devel] any interest in a BiocMatrix core package?

> Sent: Saturday, 25 February 2017 8:34:58 AM To: Aaron Lun Cc: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>> Subject: Re: [Bioc-devel] any interest in a BiocMatrix core package? yes the DelayedArray fr

Re: [Bioc-devel] any interest in a BiocMatrix core package?

~ > > > Kylie Ariel Bemis > > > Future Faculty Fellow > > > College of Computer and Information Science > > > Northeastern University > > > kuwisdelu.github.io<http://kuwisdelu.github.io/><https:// > > kuwisdelu.github.io<https://kuwisdelu.

Re: [Bioc-devel] any interest in a BiocMatrix core package?

M, Aaron Lun <a...@wehi.edu.au<mailto:alun@ >>> > wehi.edu.au>> wrote: >>> > >>> > It's a good place to start, though it would be very handy to have a >>> C(++) >>> > API that can be linked against. I'm not sure how muc

Re: [Bioc-devel] any interest in a BiocMatrix core package?

. I'm not sure how much work that would >> > entail but it would give downstream developers a lot more options. Sort >> of >> > like how we can link to Rhtslib, which speeds up a lot of BAM file >> > processing, instead of just relying on Rsamtools. >> > >> &g

Re: [Bioc-devel] any interest in a BiocMatrix core package?

how we can link to Rhtslib, which speeds up a lot of BAM file > > processing, instead of just relying on Rsamtools. > > > > > > -Aaron > > > > ________ > > From: Tim Triche, Jr. <tim.tri...@gmail.com<mailto:tim.tri...@gmail.com >

Re: [Bioc-devel] any interest in a BiocMatrix core package?

; > Sent: Saturday, 25 February 2017 8:34:58 AM > To: Aaron Lun > Cc: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> > Subject: Re: [Bioc-devel] any interest in a BiocMatrix core package? > > yes > > the DelayedArray framework that handles HDF5Array, etc. seems l

Re: [Bioc-devel] any interest in a BiocMatrix core package?

riche, Jr.; bioc-devel@r-project.org Subject: Re: [Bioc-devel] any interest in a BiocMatrix core package? What is the data type for an expression value? Is it assumed that double precision will be needed? On Fri, Feb 24, 2017 at 4:50 PM, Aaron Lun <a...@wehi.edu.au<mailto:a...@wehi.edu.au>&

Re: [Bioc-devel] any interest in a BiocMatrix core package?

From: Vincent Carey <st...@channing.harvard.edu> >> Sent: Saturday, 25 February 2017 9:25 AM >> To: Aaron Lun >> Cc: Tim Triche, Jr.; bioc-devel@r-project.org >> Subject: Re: [Bioc-devel] any interest in a BiocMatrix core package? >> >> What

Re: [Bioc-devel] any interest in a BiocMatrix core package?

). -Aaron From: Vincent Carey <st...@channing.harvard.edu> Sent: Saturday, 25 February 2017 9:25 AM To: Aaron Lun Cc: Tim Triche, Jr.; bioc-devel@r-project.org Subject: Re: [Bioc-devel] any interest in a BiocMatrix core package? What is the data type for an expr

Re: [Bioc-devel] any interest in a BiocMatrix core package?

t; Sent: Saturday, 25 February 2017 8:34:58 AM To: Aaron Lun Cc: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> Subject: Re: [Bioc-devel] any interest in a BiocMatrix core package? yes the DelayedArray framework that handles HDF5Array, etc. seems like the right choice? --t On Fri

Re: [Bioc-devel] any interest in a BiocMatrix core package?

On Fri, Feb 24, 2017 at 1:26 PM, Aaron Lun wrote: > Hi everyone, > > > I was thinking of something that you could supply any supported matrix > representation to a registered function via .Call; the C++ constructor > would recognise the type of matrix during class

Re: [Bioc-devel] any interest in a BiocMatrix core package?

;st...@channing.harvard.edu> Sent: Saturday, 25 February 2017 9:25 AM To: Aaron Lun Cc: Tim Triche, Jr.; bioc-devel@r-project.org Subject: Re: [Bioc-devel] any interest in a BiocMatrix core package? What is the data type for an expression value? Is it assumed that double precision will be needed? On Fri,

Re: [Bioc-devel] any interest in a BiocMatrix core package?

_ > From: Tim Triche, Jr. <tim.tri...@gmail.com> > Sent: Saturday, 25 February 2017 8:34:58 AM > To: Aaron Lun > Cc: bioc-devel@r-project.org > Subject: Re: [Bioc-devel] any interest in a BiocMatrix core package? > > yes > > the DelayedArray framework that hand

Re: [Bioc-devel] any interest in a BiocMatrix core package?

processing, instead of just relying on Rsamtools. -Aaron From: Tim Triche, Jr. <tim.tri...@gmail.com> Sent: Saturday, 25 February 2017 8:34:58 AM To: Aaron Lun Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] any interest in a BiocMatrix core package

Re: [Bioc-devel] any interest in a BiocMatrix core package?

yes the DelayedArray framework that handles HDF5Array, etc. seems like the right choice? --t On Fri, Feb 24, 2017 at 1:26 PM, Aaron Lun wrote: > Hi everyone, > > I just attended the Human Cell Atlas meeting in Stanford, and people were > talking about gene expression

Re: [Bioc-devel] any interest in a BiocMatrix core package?

Hi everyone, I just attended the Human Cell Atlas meeting in Stanford, and people were talking about gene expression matrices for >1 million cells. If we assume that we can get non-zero expression profiles for ~5000 genes, we�d be talking about a 5000 x 1 million matrix for the raw count data.