GO-PCA Demo "DMAP"

Author: Florian Wagner
Email: florian.wagner@duke.edu

Overview

In this demo, GO-PCA (Wagner, 2015) is applied to the DMAP dataset (Novershtern et al., 2011). The demo consists of a Jupyter notebook (01 - Demo.ipynb) that contains a series of analysis steps. For each step, the notebook shows the commands/code executed along with the corresponding output. For more information about Jupyter notebooks, see the Project Jupyter homepage.

Viewing the demo

The notebook can be viewed online using nbviewer.

Re-running the demo

Jupyter notebooks are inherently executable. It is therefore possible to re-run all the code in this demo, thereby reproducing all of the results shown. Clone or download this repository, and make sure that:

• Python is installed (preferably Python 3.5 or 3.6, but Python 2.7 should work, too).

• The GenomeTools (v0.2.1) and GO-PCA (v0.2.0) Python packages are installed. To quickly install these packages, run the following on the command line:

  > pip install --user genometools==0.2.1 gopca==0.2.0

• The Jupyter Python package is installed and the Jupyter server is running. To quickly do this, run the following two commands on the command line:

  > pip install --user jupyter
  > jupyter notebook
  

  The second command should open a browser window showing your file system. Browse to where you downloaded this repository and open the "01 - Demo" notebook. You should now be able to re-run the demo by selecting "Cell->Run All" from the menu.

Feedback, bugs, and improvements

Please feel free to email Florian Wagner for feedback, and/or use the GitHub issue system to report bugs and suggest improvements.

Copyright and License

Copyright (c) 2016 Florian Wagner.

This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.