https://github.com/lolab-msm/magine
Mechanism of Action Generation involving Network Analysis
https://github.com/lolab-msm/magine
Last synced: about 1 year ago
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Mechanism of Action Generation involving Network Analysis
- Host: GitHub
- URL: https://github.com/lolab-msm/magine
- Owner: LoLab-MSM
- License: gpl-3.0
- Created: 2016-05-09T19:26:13.000Z (about 10 years ago)
- Default Branch: master
- Last Pushed: 2022-12-27T15:36:57.000Z (over 3 years ago)
- Last Synced: 2025-05-09T00:39:23.621Z (about 1 year ago)
- Language: Jupyter Notebook
- Homepage:
- Size: 477 MB
- Stars: 9
- Watchers: 7
- Forks: 5
- Open Issues: 4
-
Metadata Files:
- Readme: README.rst
- License: LICENSE
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README
=================================================================
MAGINE : Mechanism of Action Generator involving Network Analysis
=================================================================
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:target: https://github.com/LoLab-VU/MAGINE/actions/workflows/build.yml
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:target: https://codecov.io/gh/LoLab-VU/MAGINE
.. image:: https://readthedocs.org/projects/magine/badge/?version=latest
:target: https://magine.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
.. image:: https://mybinder.org/badge.svg
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.. image:: https://badges.gitter.im/LoLab-VU/MAGINE.svg
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:alt: Join the chat at https://gitter.im/LoLab-VU/MAGINE
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.
.. _Anaconda: https://www.anaconda.com/distribution/#download-section
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!