[Bioc-devel] Dependency to PEER

Christian Mertes merte@ @ending from in@tum@de
Tue Sep 25 18:40:12 CEST 2018

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!


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