[Bioc-devel] Citation of an accompanying paper

[Alina Selega]

This is very useful, thank you very much! I will stay tuned for any further
advice on this.

Thanks,
Alina

On 22 March 2017 at 16:53, Gabe Becker <becker.gabe at gene.com> wrote:

> Alina,
>
> Typically in cases like the one you describe, people want users to use the
> paper citation when citing use of the package. Whether this is what they
> "should" want is somewhat debatable, but at least it seems reasonable, as
> by using the package users are, assumedly, applying the method your package
> implements.
>
> That said, a package can (from a mechanical perspective) have list more
> than one citation in it's CITATION file. Xie's knitr does this, for example
> (seehttps://github.com/yihui/knitr/blob/master/inst/CITATION and what is
> returned from citation(package="knitr") ) .
>
> Whether it's good to do this, and more generally whether package users
> should be expected to cite a (theory-based) methods paper and software
> which implements the method, particularly when they are by the same author,
> is again debatable. I have my thoughts on that but it's somewhat tangential
> to your question.
>
> It might be valuable for the Bioconductor team to have guidelines/an
> official view of how to navigate these issues.
>
> Best,
> ~G
>
> On Wed, Mar 22, 2017 at 9:36 AM, Kasper Daniel Hansen <
> kasperdanielhansen at gmail.com> wrote:
>
>> If you do not have a CITATION file, a citation is automatically generated.
>> So yes, effectively it would overwrite.  See details in R-exts.
>>
>> On Wed, Mar 22, 2017 at 6:30 AM, Alina Selega <alina.selega at gmail.com>
>> wrote:
>>
>> > Hi Monther,
>> >
>> > Thank you for your reply!
>> >
>> > Would that overwrite the package citation that currently shows up on the
>> > page though? My paper doesn't cite the Bioconductor package (as it was
>> > accepted before I had a valid link to include), it just refers to the
>> same
>> > name of the computational method. Is there a way to include both
>> citations?
>> > And if not, which one should I keep?
>> >
>> > Thanks,
>> > Alina
>> >
>> > On 21 March 2017 at 22:13, Monther Alhamdoosh <m.hamdoosh at gmail.com>
>> > wrote:
>> >
>> > > Hi Alina,
>> > >
>> > > I think you need to add a file named CITATION in your package (usually
>> > > under the inst folder) and use bibentry as follows
>> > >
>> > > bibentry(bibtype = "Article",
>> > >
>> > >          title = "Combining multiple tools outperforms individual
>> methods
>> > > in gene set enrichment analyses",
>> > >
>> > >          author = c(person("Monther", "Alhamdoosh"),
>> > >
>> > >                     person("Milica", "Ng"),
>> > >
>> > >                     person("Nicholas", "Wilson"),
>> > >
>> > >                     person("Julie", "Sheridan"),
>> > >
>> > >                     person("Huy", "Huynh"),
>> > >
>> > >                     person("Michael", "Wilson"),
>> > >
>> > >                     person("Matthew", "Ritchie")),
>> > >
>> > >          journal = "Bioinformatics",
>> > >
>> > >          page = "414-424",
>> > >
>> > >          volume = 33,
>> > >
>> > >          number = 3,
>> > >
>> > >          year = 2017,
>> > >
>> > >          doi = "10.1093/bioinformatics/btw623")
>> > >
>> > >
>> > >
>> > > Cheers,
>> > >
>> > > Monther
>> > >
>> > > On Wed, Mar 22, 2017 at 8:11 AM, Alina Selega <alina.selega at gmail.com
>> >
>> > > wrote:
>> > >
>> > >> Hi,
>> > >>
>> > >> My methods paper (doi:10.1038/nmeth.4068) associated with my package
>> > >> BUMHMM
>> > >> was accepted before I submitted the package for revision at
>> > Bioconductor.
>> > >> I
>> > >> would like the package page to also hold the citation to the paper.
>> What
>> > >> is
>> > >> the best way to add this paper citation? (I cite it in the vignette,
>> but
>> > >> it
>> > >> would be nice to also have it on the main page.)
>> > >>
>> > >> Thank you,
>> > >> Alina Selega
>> > >>
>> > >>         [[alternative HTML version deleted]]
>> > >>
>> > >> _______________________________________________
>> > >> Bioc-devel at r-project.org mailing list
>> > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> > >>
>> > >
>> > >
>> >
>> >         [[alternative HTML version deleted]]
>> >
>> > _______________________________________________
>> > Bioc-devel at r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
>>
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>>
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>
>
>
> --
> Gabriel Becker, Ph.D
> Associate Scientist
> Bioinformatics and Computational Biology
> Genentech Research
>

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