ellimilial / diamond

DIseAse MODule identification algorithim

DIAMOnD

DIAMOnD.py runs the DIAMOnD algorithm as described in

A DIseAse MOdule Detection (DIAMOnD) Algorithm derived from a systematic analysis of connectivity patterns of disease proteins in the Human Interactome. PlOS Comp Bio (in press), 2015.

by Susan Dina Ghiassian, Joerg Menche & Albert-Laszlo Barabasi

The DIAMOnD website can be found at:

Instruction to use the source code:

1. Download the code.
2. Make sure to make the code executable by chmod +x DIAMOnD.py
3. Run the code (./DIAMOnD.py in command line or “run DIAMOnD.py" in ipython). This will bring up the correct usage of the code.
4. Run the code according the suggested usage and input files description(See below).

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Directory Example

contains two input files:

1. seed_genes.txt (list of genes associated with a phenotype of interest)
2. PPI.txt (Protein-protein interaction network. note that gene IDs should be consistent in the two input files) The following command will generate the first 100 DIAMOnD nodes and save them in a file) ./DIAMOnD.py PPI.txt seed_genes.txt 100