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SystemsGenetics / KINC

Knowledge Independent Network Construction
MIT License
11 stars 4 forks source link

Filtering #185

Closed spficklin closed 2 years ago

spficklin commented 2 years ago

This PR makes some fixes to the R an Python scripts. It also adds two new scripts. One for creating linked communities after the network is created and another for converting a KINC network into a GraphML file.

Also, the PR makes some fixes to the 3D viewer.

spficklin commented 2 years ago

@bentsherman. If you want to check these changes out I'll leave them in this PR for a while. If not, I'll merge after some time.

bentsherman commented 2 years ago

Looks good to me. My only comment is that KINC can extract networks in GraphML format, but I see why you need it. Need to convert after all of the extra filtering scripts. Perhaps we should remove the GraphML support from KINC in the future if it will never be used?

spficklin commented 2 years ago

Thanks for the quick review @bentsherman . My hope is that one day we can get these filtering steps integrated into KICN directly. I needed the graphML converter to be able to load networks into Tripal via the https://github.com/tripal/tripal_network and since that module will be shared publically others will need it to... hence the addition.