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.cast...@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 <mer...@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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