Hi Hervé,
Thank you for your comment and for looking into our package – it would
definitely make sense to try and not depend on clusterProfiler if it is that
heavy of a dependency (and we don’t use it so much as you mention), more in
general working in the direction of removing little-used or
Hi Bioconductor team member,
Hope you are doing well! My name is Lihe Liu, and we are a computational
biology team from Animal & Dairy Science Department at UW-Madison.
We have great interests in separate logic and data in our R package development
by integrating AnnotationHub.
I went over
On 10/12/23 00:45, Matteo Tiberti wrote:
Hi Hervé,
Thank you for your comment and for looking into our package – it would
definitely make sense to try and not depend on clusterProfiler if it
is that heavy of a dependency (and we don’t use it so much as you
mention), more in general working
Hi,
one of the kind of tools that Hervé is referring to is the package
BiocPkgTools:
https://bioconductor.org/packages/BiocPkgTools
section "7 Dependency burden" in the vignette illustrates how to
identify dependencies that you might want to get rid of.
cheers,
robert.
On 12/10/23
On 10/12/23 12:25, Zuguang Gu wrote:
> The devel version of DOSE depends on MPO.db.
>
> I also found MoonlightR depends on DOSE only on its two functions:
> gseDO() and simplot().
>
> An analysis by the pkgndep package shows if you can reduce the
> dependency on both clusterProfiler and DOSE, a
The devel version of DOSE depends on MPO.db.
I also found MoonlightR depends on DOSE only on its two functions: gseDO()
and simplot().
An analysis by the pkgndep package shows if you can reduce the dependency
on both clusterProfiler and DOSE, a total of 46 upstream dependencies will
be reduced
There did seem to be an issue with the Annotation resource AH111553 that was
preventing MPO.db from being installed. I've refreshed it and reinstalled
MPO.db. I was able to manually install MoonlightR, Moonlight2R, as well as some
of the other packages you mentioned after these changes. We
