Re: [Bioc-devel] Citation of an accompanying paper

2017-03-22 Thread 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 wrote: > Alina, > > Typically in cases like the one you describe, people want users to use the > paper citation when citing use of the package. Whethe

Re: [Bioc-devel] Citation of an accompanying paper

2017-03-22 Thread Leonardo Collado Torres
You can include both like I do in https://github.com/leekgroup/derfinderPlot/blob/master/inst/CITATION which is similar to what Xie's knitr does. On Wed, Mar 22, 2017 at 12:53 PM, Gabe Becker wrote: > Alina, > > Typically in cases like the one you describe, people want users to use the > paper ci

Re: [Bioc-devel] Citation of an accompanying paper

2017-03-22 Thread Gabe Becker
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 p

Re: [Bioc-devel] Citation of an accompanying paper

2017-03-22 Thread Kasper Daniel Hansen
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 wrote: > Hi Monther, > > Thank you for your reply! > > Would that overwrite the package citation that currently

Re: [Bioc-devel] Citation of an accompanying paper

2017-03-22 Thread Alina Selega
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 the

Re: [Bioc-devel] Citation of an accompanying paper

2017-03-21 Thread Monther Alhamdoosh
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(perso

[Bioc-devel] Citation of an accompanying paper

2017-03-21 Thread Alina Selega
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 vignett