Bishoy Wadie
Bishoy Wadie
## PR checklist Closes #5333 - [X] This comment contains a description of changes (with reason). - [X] If you've fixed a bug or added code that should be tested,...
### Is there an existing module for this? - [x] I have searched for the existing module ### Is there an open PR for this? - [x] I have searched...
## PR checklist Closes #3085 - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should...
Create a container for [decoupleR](https://saezlab.github.io/decoupleR/articles/tf_bk.html) to use in nf-core modules
https://metaspace2020.eu/project/cc9ebe2a-0876-11ef-86c1-d322eda885b4?tab=datasets
Based on the current formulation of the FDR, datasets having high decoy scores can lead to FDR values > 1 leading to loss of some annotations when preparing results by...
Having CHNOPS based adducts will increase the chance for a generated decoy ion to be isomeric or isobaric to an ion of a real molecule. As this affects the FDR...
We can either add 3 intensity columns instead of 1 which would be informative to the user, but probably will slow down the request, or allow the user to choose...
https://github.com/metaspace2020/metaspace/blob/6b129f9bb83232c347b57ab69d52b0377aaf0151/docker/setup-dev-env.sh#L26  Can we ensure that if database already exists that it won't download it again ?. It will invoke the assertion error below https://github.com/metaspace2020/metaspace/blob/c36571e0893295c30fb8b1b67e04886e27e373f0/metaspace/engine/sm/engine/db.py#L114 When I run https://github.com/metaspace2020/metaspace/blob/c36571e0893295c30fb8b1b67e04886e27e373f0/metaspace/engine/scripts/import_lion_info.py#L53C13-L53C77
I don't see the arguments `scaleTOMs`, `scaleQuantile`, and `sampleForScaling` in `WGCNA::blockwiseConsensusModules`. Don't you mean the following params : networkCalibration = c("single quantile", "full quantile", "none"), # Simple quantile calibration options...