gemmapy: a Python Wrapper for the Gemma API

This is a Python wrapper for Gemma <https://gemma.msl.ubc.ca/>'s RESTful API <https://gemma.msl.ubc.ca/resources/restapidocs/>. Gemma is a web site, database and a set of tools for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles. Gemma contains data from thousands of public studies, referencing thousands of published papers.

Installation instructions

.. This is a content of docs/install.rst. Update it whenever install.rst changes.

The package requires Python3.10+.

. Install it from a local copy

.. code-block:: bash

  git clone git@github.com:PavlidisLab/gemmapy.git
  cd gemmapy
  pip install .

. Install it from PyPI

.. code-block:: bash

  pip install gemmapy

Usage

To get started with gemmapy, read the Tutorial <https://pavlidislab.github.io/gemmapy/tutorial.html>_.

The full documentation can be found at https://pavlidislab.github.io/gemmapy/.

Citation

To cite Gemma, please use: Lim, N. et al., Curation of over 10 000 transcriptomic studies to enable data reuse, Database, 2021 <https://doi.org/10.1093/database/baab006>_.