The goal of this repository is to document all the tools made available specifically in the loos_group-AUDIT folder on Esrum. You can find information on the tools and tutorials to run them under the different folders in this repository.
✏️ NOTE: Please note that you need to be added to the loos_group-AUDIT folder on Esrum to be able to access and run the tools described in this repository. If you have not already been added to this folder, then contact me for help.
Once you have been added to the loos_group-AUDIT folder, you will have a personal folder available inside /projects/loos_group-AUDIT/people/ with your KU username. This folder is only accessible by you, and it is the recommended folder to perform analysis and store data.
You can copy over the scripts from /projects/loos_group-AUDIT/data/tutorials/ to your personal folder and modify the paths to your files. The paths to tool-specific data do not need to be modified, as this data is stored in a commonly accessible folder i.e., /projects/loos_group-AUDIT/data/tool_data/. Please refrain from modifying the original tool data and template scripts.
- Polygenic Priority Score (PoPS) v0.2
- MAGMA
- Fine-mapped Locus Assessment Model of Effector geneS (FLAMES) v.1.1.2 (tutorial incomplete)
- SBayesRC
- RSIDBuildTranslator - A tool to that annotates genetic data with rsIDs, or chromosome and position from GRCh37 or GRCh38, using whichever is available in your data.
- cS2G
Please contact me if you need help or have any suggestions/feedback/ideas :)
Siddhi Jain siddhi.jain@sund.ku.dk