Open MrHedmad opened 1 year ago
I want to add that the annotation module could be split from BioTEA if we make a small tool to interact with BioMart. Something simple and from the command line that could add annotations from BioMart given a .csv
file with ENSGs. This would allow the user to easily add a variety of annotations (and not just those given by biotea annotate
), and it would not be limited to BioTEA.
If we move to ENSGs, then the gene symbols should be hot-downloaded from BioMart at runtime.
Looking at the issues again, this was already mentioned in a bioTEA issue: https://github.com/CMA-Lab/bioTEA/issues/1
This issue was raised by @Feat-FeAR :
The internal annotations for human chips do not have linked scripts for re-generation. Additionally, there are other considerations to make: