Python port of g:ProfileR, the R wrapper for the g:Profiler functional enrichment tool.

Just like the R wrapper, it simply sends an HTTP request to http://biit.cs.ut.ee/gprofiler/ and parses the text-only version of the results.

You can simply install python-gprofiler by doing

pip install gprofiler

It requires requests and pandas.

The ability to fetch a .png representation of the results is not implemented as I don't see a use for it. Biogrid interaction graphs are also not parsed since I never use those and am not sure how to parse them correctly.

Once the package is installed, here is an example of what to expect when running it in IPython:

In [1]: from gprofiler import gprofiler

In [2]: enrichment = gprofiler(['Klf4', 'Pax5', 'Sox2', 'Nanog'], organism='mmusculus')

In [3]: enrichment.sort_values('p.value').head()
Out[3]: 
            query.number significant   p.value  term.size  query.size  \
term.id                                                                 
GO:0032526             1        True  0.000100         78           4   
GO:0000976             1        True  0.000210        549           4   
GO:0048598             1        True  0.000258        578           4   
GO:0044212             1        True  0.000519        688           4   
GO:0000975             1        True  0.000531        692           4   

            overlap.size  recall  precision     term.id domain  \
term.id                                                          
GO:0032526             3    0.75      0.038  GO:0032526     BP   
GO:0000976             4    1.00      0.007  GO:0000976     MF   
GO:0048598             4    1.00      0.007  GO:0048598     BP   
GO:0044212             4    1.00      0.006  GO:0044212     MF   
GO:0000975             4    1.00      0.006  GO:0000975     MF   

            subgraph.number  \
term.id                       
GO:0032526                9   
GO:0000976                6   
GO:0048598                2   
GO:0044212                6   
GO:0000975                6   

                                                    term.name  relative.depth  \
term.id                                                                         
GO:0032526                          response to retinoic acid               2   
GO:0000976        transcription regulatory region sequence...               4   
GO:0048598                            embryonic morphogenesis               1   
GO:0044212        transcription regulatory region DNA binding               3   
GO:0000975                      regulatory region DNA binding               2   

                    intersection  
term.id                           
GO:0032526       KLF4,NANOG,SOX2  
GO:0000976  KLF4,NANOG,PAX5,SOX2  
GO:0048598  KLF4,NANOG,PAX5,SOX2  
GO:0044212  KLF4,NANOG,PAX5,SOX2  
GO:0000975  KLF4,NANOG,PAX5,SOX2