A tool to generate prioritized genes using phenotype information.
- Available at: http://molgenis.org/vibe
- Source code: https://github.com/molgenis/molgenis-app-vibe
- Download vibe .jar file
- Download and extract TDB
- Make sure you have Java 8 or higher
- Open a terminal and run VIBE.
java -jar vibe-1.0.jar -v -t TDB/ -o results.tsv -p HP:0002996 -p HP:0001377
Instructions regarding building/testing the app can be found here and how to create a TDB for the app can be found here.
* = Only required when certain arguments are used.
java -jar vibe-with-dependencies.jar [-h] [-v] -t <FILE> [-w <FILE> -n <NAME> -m <NUMBER>] -o <FILE> [-s <NAME>] [-l] -p <HPO ID> [-p <HPO ID>]...
Using only the user-defined phenotypes with the output being sorted based on the highest gene-disease association score present per gene:
java -jar vibe-with-dependencies.jar -v -t TDB/ -s gda_max -o results.tsv -p HP:0002996 -p HP:0001377
Output file:
+630 more lines
Using the user-defined phenotypes and phenotypes that are related to them with a maximum distance of 1 with the output sorted based on the Disease Specificity Index:
java -jar vibe-with-dependencies.jar -v -t TDB/ -w hp.owl -n distance -m 1 -s dsi -o results.tsv -p HP:0002996
Output file:
+2711 more lines
Using the user-defined phenotypes and their (grand)children with a maximum distance of 2 with the output sorted based on the Disease Pleiotropy Index:
java -jar vibe-with-dependencies.jar -v -t TDB/ -w hp.owl -n children -m 2 -s dpi -o results.tsv -p HP:0002996
Output file:
+974 more lines
Q: It takes forever to retrieve information from the TDB.
A: Depending on the how much information needs to be retrieved from the TDB based on the input genes, this process may indeed take a while. However, there are ways to speed up this process. Examples include using an SSD instead HDD and using a 64-bit JVM.