With the extensive update of g:Profiler toolset we have also implemented a new R package gprofiler2 to comply with the changes. Our previous R package, gProfileR (https://cran.r-project.org/web/packages/gProfileR/index.html) does not have access to our most recent data (it uses data from October 2018) and therefore will not be developed further. We consider this as a deprecated package.

Compared to the old gProfileR package, the gprofiler2 introduces some changes to the input parameters and output structure. In addition, a broader range of visualisation possibilities for publication-quality images is now available in gprofiler2 package.

For example, the differences in running the default example of the enrichment tool g:GOSt:
In gProfileR: 
gp = gprofiler(c("Klf4", "Pax5", "Sox2", "Nanog"), organism = "mmusculus")
Here the result gp is a data.frame().

In gprofiler2: 
gp = gost(c("Klf4", "Pax5", "Sox2", "Nanog"), organism = "mmusculus")
Here the result gp is a named list where gp$result will return the data.frame() with the results and gp$meta includes all the query related metadata for reproducibility.

For the full documentation see https://cran.r-project.org/web/packages/gprofiler2/gprofiler2.pdf

Please feel free to contact us via the contact page or via email at biit.support@ut.ee if you need any assistance in switching your code over to gprofiler2.