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:
- Download the code.
- Make sure to make the code executable by chmod +x DIAMOnD.py
- Run the code (./DIAMOnD.py in command line or “run DIAMOnD.py" in ipython). This will bring up the correct usage of the code.
- Run the code according the suggested usage and input files description(See below).
Directory Example
contains two input files:
- seed_genes.txt (list of genes associated with a phenotype of interest)
- 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