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Answer: Reading vcf file with readVcf by James W. MacDonald 58k

Usually when you run out of RAM, you usually get an error saying that 'R couldn't allocate a vector of size <some number>'. When it just sa…

Answer: Genic annotations of whole hg38 by James W. MacDonald 58k

What exactly do you mean by 'proportion of genic annotations'? One possibility would be to see what proportion of all the exons are covered…

Answer: Understanding output of Negative Binomial in DESeq2 by Michael Love 34k

> Does this mean that there are seven genes in total that will have significant adjusted p-value? yes > i recall when multiple linea…

Answer: VST transformation and covariates in the TCGA TARGET GTEx dataset by Michael Love 34k

The above sounds fine to me. I do not recommend adding 1 to all expected counts for DESeq2. It is strange that every gene contains a …

Answer: Swish direction of comparison based on order of factors by Michael Love 34k

hi Jean, Thanks for the question, this wasn't explicitly stated in the documentation, so I've updated it, here are the new sections in m…

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Answer: Swish direction of comparison based on order of factors

Comment: Gradient dotplot

Answer: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi

Answer: Effect size using likelihood ratio test in DESeq2

Comment: ggtree install

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Scholar to Gordon Smyth 43k

Popular Question to Dario Strbenac ★ 1.5k

Popular Question to Hans-Ulrich Klein ▴ 330