kmoon3 / magic Goto Github PK

MAGIC has been implemented in Python3 and Matlab.

1. The Python3 version of MAGIC can be installed using:

    $> git clone git://github.com/pkathail/magic.git
    $> cd magic
    $> sudo -H pip3 install .
   

2. MAGIC depends on a number of python3 packages available on pypi and these dependencies are listed in setup.py All the dependencies will be automatically installed using the above commands

A tutorial on MAGIC usage and results visualization for single cell RNA-seq data can be found in this notebook: http://nbviewer.jupyter.org/github/pkathail/magic/blob/develop/notebooks/Magic_single_cell_RNAseq.ipynb

A python GUI is now available for MAGIC. After following the installation steps listed below, the GUI can be invoked using

    $> magic_gui.py

1. Matlab implementation of MAGIC uses Mauro Maggioni's Diffusion Geometry code. Download from here: http://www.math.jhu.edu/~mauro/Code/DiffusionGeometry_01.zip or use included DiffusionGeometry_01.zip
2. test_magic.m shows how to run MAGIC. Also included is a function for loading 10x format data (load_10x.m)