Library for programmatically interacting with GenePattern from Python.

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  • License: BSD
  • Author: Thorin Tabor
  • Tags genepattern, genomics, bioinformatics
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Project description

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GenePattern Python Library

This is a Python library for working with GenePattern programmatically. Behind the scenes, calls from this library execute the GenePattern REST API.

Supported Python Versions

This library requires Python 3.6+. The bundled data submodule gp.data also requires pandas, although the rest of the module does not.

Python 2 Support: Support for Python 2 was removed in version 1.4.0. Python 2 users should use version 1.3.1.

Installing

It is recommended to install this library from PIP. Simply execute the command below:

pip install genepattern-python

Upgrading

To upgrade to the latest version of the library, execute the command below:

pip install genepattern-python --upgrade

Tutorial

A tutorial on how to use the GenePattern Python Library is available here.

"Connection Reset by Peer" Error

Connecting to the GenePattern public server now requires TLS 1.2+. Older versions of SSL and TLS will no longer work. If you're attempting to connect and receiving a "Connection Reset by Peer" error, you will need to update the OpenSSL library associated with your Python installation.

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