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.
The manual is available online at http://magine.readthedocs.io.
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
pipto 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.
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.
Install MAGINE
The installation is very straightforward with
pip- type the following in a terminal:$ pip install magine
Start Python and MAGINE
From the terminal or command prompt type
$ jupyter notebook
You will then be at the Python prompt. Type
import magineto try loading magine. If no error messages appear and the next Python prompt appears, you have succeeded in installing magine!