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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…

Comment: IsoformSwitchAnalyzeR package on mouse data by bpshtiwan ▴ 10

Hello Ryan, Also, I am not able to find esemble file that has haplotype info in it. Kindly, have you solved the problem? Best

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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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