A_Skelton73
  • Member for 4 years, 8 months
  • Last seen more than a month ago
  • Newcastle upon Tyne, United Kingdom
Can I model technical replicates in DESeq2?
5 votes

If they're truly technical replicates, then there's no way to model them using DESeq2*, as you've alluded to with the collapseReplicates function. DESeq2/ Mike Love's general recommendation with ...

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How can I use annotations to remove variants not relevant to cancer risk?
5 votes

While your question is specific to cancerous germline mutations, I'd suggest you look at the COSMIC database of somatic mutations to include in your analysis. There are other factors to include in ...

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Deciding which samples go in which batch
2 votes

I've had to go through this pain, and found the best way to do it was to simulate the model fit to start assessing the balance of covariates. I've got two notebooks available on Github, which should ...

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