Re: [Bioc-devel] Compatibility of Bioconductor with tidyverse S3 classes/methods

2020-02-08 Thread stefano
Thanks again. *To Martin.* Got the point and I agree. I will do my best. *To Vincent. * I see. At the moment ttBulk is an API for users, not yet for developers. But I can already imagine an API framework where you can feed a new custom functionality (let's say UMAP dimensionality reduction

Re: [Bioc-devel] how to trace 'Matrix' as package dependency for 'GenomicScores'

2020-02-08 Thread Martin Morgan
I find it quite interesting to identify formal strategies for removing dependencies, but also a little outside my domain of expertise. This code library(tools) library(dplyr) ## non-base packages the user requires for GenomicScores deps <- package_dependencies("GenomicScores", db,

Re: [Bioc-devel] Compatibility of Bioconductor with tidyverse S3 classes/methods

2020-02-08 Thread Martin Morgan
The first thing is that most contributed packages end up being accepted, so the discussion here should be considered as (strong) advice, rather than requirement. The advice is partly offered to maximize the success of contributed packages in the Bioconductor ecosystem, but at the end of the day

Re: [Bioc-devel] Compatibility of Bioconductor with tidyverse S3 classes/methods

2020-02-08 Thread Vincent Carey
On Fri, Feb 7, 2020 at 6:39 PM stefano wrote: > Thanks Guys for the discussion (I am learning a lot), > > *To Martin:* > > Thanks for the tips. I will start to implement those S4 style methods > https://github.com/stemangiola/ttBulk/issues/7 > > I would *really *like to be part of Bioconductor