[Bioc-devel] Dependency to PEER

[Christian Mertes]

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.castelo using 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 <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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