[Bioc-devel] Dependency to PEER

[Christian Mertes]

Hi Martin Morgen,

Thanks for the suggestion with the vignette. This will do it.

Best,
Christian

> On 26. Sep 2018, at 04:07, Martin Morgan <mtmorgan.bioc using gmail.com> wrote:
> 
> 
> 
> On 09/25/2018 07:07 PM, Christian Mertes wrote:
>> 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.
> 
> not sure what that means; better not to be devious if that is what 'special' means.
> 
> I think an appropriate thing to do would be to illustrate installation / evaluation functionality in a non-evaluated code chunk in the vignette. Your reviewer will be understanding.
> 
> Martin
> 
>> 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
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>>         [[alternative HTML version deleted]]
>>>>> 
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