[Bioc-devel] Dependency to PEER

Kasper Daniel Hansen k@@perd@nielh@n@en @ending from gm@il@com
Tue Sep 25 18:55:01 CEST 2018

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 <mertes using 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
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