MAGMA Gene set enrichment analysis using uploaded summary stats

[Per Qvist]

Could you consider adding a MAGMA gene-set enrichment analysis option to the gene2function pipeline?

It would be particularly useful, if users could upload their own summary stats like in the SNP2gene pipeline.

Thanks for a great tool!

[Kyoko Watanabe]

Hi Per,

Thank you for your suggestions.

However, MAGMA analysis is not suitable for GENE2FUNC since MAGMA requires sumstats while input of GENE2FUNC process is just a list of genes.

MAGMA gene-set analysis is performed as part of SNP2GENE, Are you asking this because you don't want to run entire SNP2GENE process but only MAGMA gene-set analysis?

I could separate MAGMA from SNP2GENE but if you just want to run MAGMA, it might be faster/easier to run MAGMA command line (it's very easy to use software, https://ctg.cncr.nl/software/magma).

Best,

Kyoko