Update to Synthetic Networks #11
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R script for parsing human interactome based on experimental evidence values R script for taking PANTHER pathways and parsing into STRING ID edge list
Now can access a list of TFs and Receptors to process a PANTHER pathway into sources and targets.
Used the function to generate Source and Target sets for 14 PANTHER pathways
…ss the data to make the combined networks (still in progress)
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@agitter The synthetic networks are be ready to use and ready for a first pass review.
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Closed in favor of #22. (I built on top of your work by Snakemake-ifying this entire script process, and converting that R script to python 👍) |
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@tristan-f-r This still needed to reviewed in general for how everything was being made. If that is going to be done in #22, that is fine, otherwise this should stay open. |
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@tristan-f-r Okay, please make a note that in #22 that the code and data for this PR #11 (and I suspect #5 as well) still needs to be fully reviewed. Whoever reviews #22 can decide on the way to break down how to review the code. |
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Added code to make synthetic data SPRAS compatible
Added code to make the threshold interactomes with uniprot accession ids
Added code to make combined networks with pathways and threshold interactomes
Added code to do overlap analytics between the pathways and threshold interactomes
Updated TF file to use reviewed/unreviewed uniprot accession ids
Updated organization of code
Updated existing code to make easier to use
In progress of updating instructions on how to use code
Removed unused code and files