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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 $\phi_j$…
Comment: TPM normalization starting with read counts by ATpoint ★ 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 • 0
I still get the same result as above, should running BiocManager::install() do the trick?
Answer: Adding custom transcript to Salmon index by ATpoint ★ 1.4k
Yes, you would add the sequence to the reference transcriptome that is used for the gentrome construction. Simply make a separate fasta fil…
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DEseq2 time-series design.
A: Importance of Order in Design Formula
remove microarray batch effects using Limma
On empirical Bayes of edgeR
Answer: CQN to DESeq2
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