[Bioc-devel] Dependency to PEER

[Robert Castelo]

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
>>
>>
>>
>>
>>          [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel using r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel