Hi Martin Morgen, Thanks for the suggestion with the vignette. This will do it.
Best, Christian > On 26. Sep 2018, at 04:07, Martin Morgan <mtmorgan.b...@gmail.com> wrote: > > > > On 09/25/2018 07:07 PM, Christian Mertes wrote: >> Hi, >> thanks for the answers. >> Since we only use 5 functions from the package within one function in our >> package, I hoped to get around it by masking this function in a special way. > > not sure what that means; better not to be devious if that is what 'special' > means. > > I think an appropriate thing to do would be to illustrate installation / > evaluation functionality in a non-evaluated code chunk in the vignette. Your > reviewer will be understanding. > > Martin > >> The package is not dependent on PEER and works without it perfectly. Its >> just to make it easier for the user if he wants to use a different >> normalisation method. >> Best, >> Christian >>> On 25. Sep 2018, at 13:39, Robert Castelo <robert.cast...@upf.edu> wrote: >>> >>> hi, >>> >>> it seems that the PEER repository hasn't been updated in the last 7 years >>> and that the package is distributed under a GPL-2 license. if i'm >>> interpreting this correctly, you could copy&paste that code into your >>> package redistributing it under the GPL-2 license and asking the users of >>> PEER to cite the PEER paper when using it. >>> >>> cheers, >>> >>> robert. >>> >>> On 25/09/2018 18:55, Kasper Daniel Hansen wrote: >>>> It is a major weakness of PEER that it has not been submitted to a standard >>>> repository. Of course, that is up to the PEER developers, but the community >>>> should put pressure on them. >>>> >>>> On Tue, Sep 25, 2018 at 12:40 PM Christian Mertes <mer...@in.tum.de> wrote: >>>> >>>>> Hi all, >>>>> >>>>> Im the developer of OUTRIDER. Our package normalises RNA-seq count data >>>>> and finds expression outliers within the population. >>>>> During the development we compared our approach against PCA and PEER. The >>>>> later one is a well established method to normalise RNA-seq data. >>>>> >>>>> https://github.com/gagneurlab/OUTRIDER < >>>>> https://github.com/gagneurlab/OUTRIDER> >>>>> https://github.com/PMBio/peer <https://github.com/PMBio/peer> >>>>> >>>>> For PEER, an R package exists on GitHub, but it is not in CRAN nor >>>>> Bioconductor, even it would fit really well with Bioconductor. >>>>> >>>>> We would like to leave the user the option to switch between the different >>>>> normalisation methods within our package (auto encoder, peer, pca, sea, >>>>> …). >>>>> But since the Bioconductor requirements are that all loaded libraries need >>>>> to be within CRAN or BioC, my question is how we should implement this. >>>>> >>>>> Is there a best practice for this? Does we have to ask the developer of >>>>> PEER to push it on CRAN or do we get around this? Or can we flag one >>>>> function to be not checked by Bioconductor for dependencies and use >>>>> require(peer) within the function? >>>>> >>>>> Thanks for any advices in advance! >>>>> >>>>> Best, >>>>> Christian >>>>> >>>>> >>>>> >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> _______________________________________________ >>>>> Bioc-devel@r-project.org mailing list >>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioc-devel@r-project.org mailing list >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >>> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
