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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 by sk • 0
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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Answer: Mapping Between GenBank ID's and Uniprot
Comment: What type of counts data to import for performing Isoform analysis in edgeR
A: Relations used in GO.db GOBPANCESTOR
Relations used in GO.db GOBPANCESTOR
Answer: RSubread output significantly different from bash Subread output
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