HPC-Atlas: Computationally Constructing A Comprehensive Atlas of Human Protein Complexes
Please install the python dependency package before running the clustering program, such as networkx, numpy and so on.
input: tab separated protein interaction network: portein-1 [tab] proein-2 [tab] weight
output: each row represents a protein complex: protein-1 [tab] ,..., protein-N
Example
pyhton3 cluster.py --input_PPI_weight ../Data/test_data/test_weight.txt --outfile ../test_outfile.txt
The "--input_PPI_weight" is the input weighted PPI network file.
The "--outfile" is the final protein complexes file.
The outfile_first is the cache file of intermediate results, which can be deleted after the program is completed.
Because the PPI file of the whole network is too large, it can only be put into Releases module and can be downloaded here: https://github.com/yul-pan/HPC-Atlas/releases
The feature matrix used in the experiment can be downloaded: https://share.weiyun.com/BFZckLjR
Since GitHub restricts the upload file to no more than 25M, please download the full version (code, data and results file) here:https://share.weiyun.com/oXupED6J
For convenience to relevant researchers, all experimental data and result files are presented in the form of UniProtID and Gene name, respectively.