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I am currently doing a project regarding gene-based analysis and gene-set analysis given a certain GWAS dataset, I only know 2 well known gene-based analysis tool which is LDSC and MAGMA.

As of now, I'm familiar with how MAGMA works, but not really sure about LDSC, I did read LDSC Wiki briefly, and I am leaning towards MAGMA atm, but it's probably just because I'm more familiar with MAGMA.

So, which one do you think is more robust? or at least what is the pros and cons of each software?

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  • $\begingroup$ Hi Andreas, do the papers describing the methods talk about the differences? If you already looked into that, you could share with us what do you think is/not different and why one/other should be better for what application. Hope it won't sound too mean, I am just wondering if the question can be more specific. $\endgroup$
    – Kamil S Jaron
    Jul 10 at 18:10

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