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