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. 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
