updated 7.0 years ago by
xiangy7
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written 7.4 years ago by
Kevin Coombes
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Answer: Retrieve gene summary start/end in biomart query
by
Mike Smith
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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
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10
To expand on what's written here: deseq2 can achieve roughly constant variance $C$ across genes by setting the per-gene dispersion $\phi_j$…
Comment: TPM normalization starting with read counts
by
ATpoint
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1.4k
Neither edgeR nor DESeq2 output TPM directly. TPM is easy to calculate though if counts and appropriate length info is available (https://s…
Comment: error running UniProt.ws
by
davi.vuko
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0
I still get the same result as above, should running BiocManager::install() do the trick?
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