I created a module for TDC that makes a knowledge graph object – https://github.com/mims-harvard/TDC/pull/207. So, pyPAGE results can be used to make gene-pathway graph and saved in TDC-KG object. Then, there are methods implemented to convert them into igraph / networkx objects. From a biology point of view, the network / graph representation compatible with these tools can enable other type of graph analysis from pypage results.
abearab
commented
1 month ago
related to https://github.com/goodarzilab/pypage/issues/30
I created a module for TDC that makes a knowledge graph object – https://github.com/mims-harvard/TDC/pull/207. So, pyPAGE results can be used to make gene-pathway graph and saved in TDC-KG object. Then, there are methods implemented to convert them into igraph / networkx objects. From a biology point of view, the network / graph representation compatible with these tools can enable other type of graph analysis from pypage results.