Functional enrichment analysis and more via the g:Profiler toolkit
Project description
The official Python 3 interface to the g:Profiler [1] toolkit for enrichment analysis of functional (GO and other) terms, conversion between identifier namespaces and mapping orhologous genes in related organisms. This library provides both a command-line tool and a Python module. It is designed to be lightweight and not require any 3rd party packages.
Besides this README, the API documentation is available [6].
Note that this used to be a Python 2 module. Since version 0.3, it has been migrated to Python 3. Please use v0.2.3 [7] in case you require Python 2 support.
Installation on Linux using pip
The pip tool [4] is the recommended method of installing Python packages.
Optionally create a virtual environment [2]:
$ virtualenv myenv $ source myenv/bin/activate
Install the software with pip, see [3] for instructions:
$ pip install gprofiler-official
Make sure that the installed gprofiler.py script is on your $PATH. When using a virtual environment as shown above, this should happen automatically.
Run an example query:
$ gprofiler.py -o scerevisiae "swi4 swi6"
For detailed usage instructions, see:
$ gprofiler.py --help
To use the module in your codebase:
from gprofiler import GProfiler gp = GProfiler("MyToolName/0.1") result = gp.gprofile("sox2")
For details, see the API documentation [6].
Installation on Linux using the tarball
You may simply download the tarball from gprofiler-official PyPI page [5], extract it and use the gprofiler.py script without installation. For detailed usage instructions, see:
$ gprofiler.py --help
You may run the test suite with:
$ python3 setup.py test
Installation on other platforms
Please see [3] for package installation instructions on various platforms.
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