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Answer: Mostly increased counts in differentially accessible peaks using DESeq2
by
Michael Love
42k
The difference between tracks and DESeq2 (or any count method in Bioc) is that tracks use simple scaling that is not robust to large shifts…
Answer: How to set filtering standard for low-expression genes in ImpulseDE2
by
Michael Love
42k
I think ImpulseDE2 is no longer part of Bioconductor (the package landing page doesn't exist). Maybe try here: https://github.com/YosefL…
Comment: Annotation for EPICv2
by
nurkenber
• 0
Thank you for your detailed reply Could you please help me understand something and I understand that it is a question best adressed to Il…
Comment: GSVA ssGSEA vs. Broad implementation of ssGSEA
by
Robert Castelo
★ 3.4k
Thanks for your analysis of the differences between ssGSEA 2.0 and ssGSEA 1.0, as I said in my previous message, please file an issue in th…
Comment: GSVA ssGSEA vs. Broad implementation of ssGSEA
by
Bob
▴ 10
Thanks for the prompt answer! I looked into the "original ssGSEA R-implementation" ([https://github.com/GSEA-MSigDB/ssGSEA-gpmodule][1]), u…
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Answer: Annotation for EPICv2
C: Vertical line at A=0, nothing else, on MA plot
Comment: RNASeq Time Course Question
Answer: RNASeq Time Course Question
Comment: limma plotMDS - logFC inverted?
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