Open tithuytrang opened 1 year ago
Hi again @tithuytrang 👋 I maintain some of the netzoo resources, so you will see me replying here and in the GitHub discussion or dispatching to other developers. So that is a great suggestion, we don't have it in the web version and I will add it as a feature request. Here is how you can do it on you own:
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 Cheers, Trang
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. -> Yes we chose to share the sample-specific networks for the database but we kept the aggregate networks for CLUEreg. We are discussing to release a nextflow of the procecessing pipeline, but this is going to take sometime since it is written in MATLAB.
Please let me know if I can help in any way.
Hi @marouenbg, Many thanks for your answers! I wonder which metric we should prioritize among the CLUEreg output statistics (Overlap, Tau, Cosine, q-values) if we would like to rank repurposing drugs based on a single value only? Also, could you be happy to offer raw data of GRAND signatures for Tau calculation? We are trying to calculate it with the PANDA results from our in vitro treatment data.
Hi @tithuytrang , I found Overlap and cosine to be quite accurate, p-value and tau are just significance values for overlap and cosine. This is the Gene targeting raw data https://granddb.s3.amazonaws.com/drugs/drugNetwork/PANDA/Drugs_Gene_Targeting_AllSamples.csv and this is TF targeting raw data https://granddb.s3.amazonaws.com/drugs/drugNetwork/PANDA/Drugs_TF_Targeting_AllSamples.csv
Please let me know if you need anything else! Marouen
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. I modified PANDA to make it work on workstations with limited RAM, using file-backed matrices to utilise hard drive space. It was a sloppy and slow workaround but we could finish analyses without HPC. It would be great if a memory-friendly option can be integrated into official releases with your optimisation.
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. As potential solutions, we thought about using a C implementation which should use very little RAM and can be bound to R/Python/MATLAB through binary routines but the old C implementation we have (https://github.com/netZoo/netZooC) is not optimal at all. So coming with a more modern C implementation can be the solution here.
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