Skip to main content
Help us improve PyPI by participating in user testing. All experience levels needed!

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_cli.py script is on your $PATH. When using a virtual environment as shown above, this should happen automatically.

Run an example query:

$ gprofiler_cli.py -o scerevisiae "swi4 swi6"

For detailed usage instructions, see:

$ gprofiler_cli.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_cli.py script without installation. For detailed usage instructions, see:

$ gprofiler_cli.py --help

You may run the test suite with:

$ python3 setup.py test

Project details


Release history Release notifications

This version
History Node

0.3.5

History Node

0.3.4

History Node

0.3.3

History Node

0.3

History Node

0.2.3

History Node

0.2.2

History Node

0.2.1

History Node

0.1.1

History Node

0.1

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
gprofiler-official-0.3.5.tar.gz (21.4 kB) Copy SHA256 hash SHA256 Source None Mar 14, 2018

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging CloudAMQP CloudAMQP RabbitMQ AWS AWS Cloud computing Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page