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 you are in the main directory where the code is.
- Run the following.
python3 DIAMOnD.py network_file seed_file n alpha(optional) outfile_name(optional)
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)
python3 DIAMOnD.py Example/PPI.txt Example/seed_genes.txt 100