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Answer: Feature Counts - potential bug with outfile.jcounts
by
Gordon Smyth
52k
The behavior you have documented in not surprising and is explained in the featureCounts documentation.
The first thing to understand is t…
Answer: Feature Counts -R XS Read Assignment Tag
by
Gordon Smyth
52k
I am not very familiar with this part of the featureCounts code, but I do not think it would be at all practical or desirable for featureCo…
Comment: Margins for gene_set_enrichment_plot
by
Leonardo Collado Torres
★
1.1k
Thanks! This one might be worth remaking with `ComplexHeatmap`. Similar to https://github.com/LieberInstitute/spatialLIBD/pull/91 that was …
Comment: DESeq2 - Comparing Comparisons
by
James W. MacDonald
67k
Full disclosure: I don't use `DESeq2`, and find the contrasts specification confusing. Because of that, I generally recommend using `result…
Comment: DESeq2 - Comparing Comparisons
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sk
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Hi James,
Thank you for your response! Quick follow-up; if I structure my contrast as below, will it perform (A-B) - (C-D)?
res_diff <…
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