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dthorbur
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[`AlphaFold3`](https://alphafoldserver.com/) (assuming you're not at conflict with their terms of use) can handle both ligands and ions. An…
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> But How could I know if the difference comes from sample instead of sequencing runs or cohort-driven batch effect?
You cannot. It's pe…
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Sorry that it was unclear in the post. The data is all CRISPR gene effect scores from DepMap. The 'significant genes' as mentioned in the p…
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king
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Thank you for your answer, it's very inspiring.
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Thanks Pierre, I was actually thinking about the duplicate PCR reads and didn't explain it properly. I have found a post mentioning that qu…
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Yes a read can be aligned more than once (I don't specifically know about gam/gaf). It would be called a "multi-mapping" read. You could im…
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allingt
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The choice of test depends on the types of variables involved and the hypothesis you have. But most importantly on the question you want am…
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I'd consider making a [block annotation](https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#block-annotation…
Comment: Comparing GSEA mutant data to wild type
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What do you mean by "significant gene"?
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From guesswork I might initiall…
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Did you perform blockwise module detection by any chance? Are your results object's contents sorted in blocks?
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The WGCNA implementation by Langfelder and Horvath provides various correlation methods to create the initial correlation matrix. I don't t…
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any idea, how can I display the labels Pre and POst on the top of the heatmap? I am looking at complexheatmap package as to how they displa…
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What p-value do you mean? When and how did you calculate it?
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What about some of the well known enhancer regions, the globin locus LCR? Likely to be highly sequenceable, and yet not on exome panels.
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