MAGINE 0.0.9

Package to analyze biological data.

MAGINE is a framework for the analysis of quantitative multi-omics data. It was designed to handle multi-sample (time points) and multi-omics (rnaseq, label-free proteomics, etc). Users are provided access to tools driven around their experimental data. Provides access to enrichment analysis, biological network construction and various visualization methods.

Documentation

The manual is available online at http://magine.readthedocs.io.

Installation

1. Install Anaconda

   Our recommended approach is to use Anaconda, which is a distribution of Python containing most of the numeric and scientific software needed to get started. If you are a Mac or Linux user, have used Python before and are comfortable using pip to install software, you may want to skip this step and use your existing Python installation.

   Anaconda has a simple graphical installer which can be downloaded from https://www.anaconda.com/distribution/#download-section - select your operating system and download the Python 3.7 version. The default installer options are usually appropriate.

2. Open a terminal

   We will install most packages with conda:

   $ conda create -n magine_env python=3.7
   $ conda activate magine_env
   $ conda config --add channels conda-forge
   $ conda install jinja2 statsmodels networkx graphviz
   $ conda install -c marufr python-igraph

   Windows users: Please download and install igraph and pycairo using the wheel files provided by Christoph Gohlke, found at https://www.lfd.uci.edu/~gohlke/ . Download and install via pip.

3. Install MAGINE

   The installation is very straightforward with pip - type the following in a terminal:

   $ pip install magine

4. Start Python and MAGINE

   From the terminal or command prompt type

   $ jupyter notebook

   You will then be at the Python prompt. Type import magine to try loading magine. If no error messages appear and the next Python prompt appears, you have succeeded in installing magine!