Markov Affinity-based Graph Imputation of Cells (MAGIC)

MAGIC has been implemented in Python3 and Matlab.

Installation and dependencies for the Python version

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

Usage

Command line

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

GUI

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

    $> magic_gui.py

Installation and dependencies for the Matlab version

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)