[Bioc-devel] Dependency to PEER

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 at 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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