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Comment: IsoformSwitchAnalyzeR package on mouse data
by
k.vitting.seerup
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100
Which version of Ensembl are you using?
Answer: Error in Create switchAnalyzeRlist
by
k.vitting.seerup
▴
100
Looks like you are supplying the wrong annotation as a GTF file.
If you look at the examples the id's the GTF annotation are called "X…
Answer: Retrieve gene summary start/end in biomart query
by
Mike Smith
★
5.7k
I'm not able to test this comprehensively today, but I think you're seeing this behaviour because you're asking for transcript level inform…
Answer: TPM normalization starting with read counts
by
Gordon Smyth
46k
> RPKM <- rpkm(y)
> But this crashed pretty quickly, might be due to the big number of genes in a dataframe (more than 20,000 genes).
`rpk…
Comment: using DESeq2 for ATAC analyses
by
eric.kern13
▴
10
To expand on what's written here: deseq2 can achieve roughly constant variance $C$ across genes by setting the per-gene dispersion $\phi_j$…
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