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
