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Calculate CLUEreg scores for new drugs #11
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Hi again @tithuytrang 👋
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That's awesome, thanks @marouenbg! Since we want to apply the same workflow as CLUEreg, could you please help with these inquiries?
We're trying to apply calculations described in the supplementary of GRAND paper so it would be very appreciated if you could provide the raw data of GRAND signatures for Tau calculation. If you prefer private discussion, my email is truongtra@deakin.edu.au |
Hello Trang,
Also, GRAND seems to have sample-specific GRNs only for drugs so would be helpful for users to get aggregated GRN for similar signature searching. Not sure if GRAND allows network contributions derived from drug-induced data? If so it would be helpful for users to have a guideline of standardised workflows used in CLUEreg.
Please let me know if I can help in any way. |
Hi @marouenbg, |
Hi @tithuytrang , Please let me know if you need anything else! |
Thanks again @marouenbg! Really appreciate your quick support. Will get back to you if I have more questions on GRAND database. A potential feature for NetZooR overall (not sure if it's suitable to post here) I think will benefit many users is RAM-friendly option. Out-of-memory R crashes greatly bar users from exploring the potential of these great packages. Some of my colleagues opted to filtering input genes (e.g., most differentially expressed only) but this might sacrifice the robustness of networks. |
Hi @tithuytrang, Thank you for this great suggestion, I thought about this a lot as well because we faced the same issue. I generally find that the Python implementation is best at RAM economy, and also running analyses in Ubuntu tends to consume the most RAM. I found that R+Ubuntu combination uses most RAM. |
Dear GRAND team,
Could there be any codes/functions to calculate CLUEreg scores (Overlap, Cosine, Tau,...) for new drugs outside of your library? We have got TF signatures for the disease using PANDA & MONSTER, but would be great to check how they are reversed comparing to those of known drugs, which are not currently available in CLUEreg but we have their expression data from in vitro treatments?
Thank you for the great work on this helpful database!
Trang
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