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Doe, Aimee
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Answer: Pre-filtering TPM kallisto for ssGSEA / DESeq2
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Michael Love
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I've seen in some papers ~1 TPM for saying something in mouse/human etc. was "minimally expressed".
For an average length gene, 10 count…
Answer: Feature Counts - potential bug with outfile.jcounts
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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
No, featureCounts cannot change the XS tag to a different tag, because that would change the information in the output. featureCounts needs…
Comment: Margins for gene_set_enrichment_plot
by
Leonardo Collado Torres
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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…
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