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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
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davi.vuko
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I still get the same result as above, should running BiocManager::install() do the trick?
Answer: Adding custom transcript to Salmon index
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ATpoint
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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
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bpshtiwan
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Hello Ryan,
Also, I am not able to find esemble file that has haplotype info in it.
Kindly, have you solved the problem?
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Comment: Design and contrast matrices for analyzing the effect of two factors of interest
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Gordon Smyth
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I understand that your mock dataset has expression data for just one protein instead of 8000, but is the phenoData complete? Does your real…
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