Bioconductor Windows

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import.bw rtracklayer Windows http

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Comment: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt? by James W. MacDonald 67k

> BTW, shouldn't you be using keep.lib.sizes = F and re-do the calcNormFactors() after filtering of the dglst low-expression ENSGs, as Gord…

Comment: Problems with oarfish + tximport + swish by Michael Love 43k

Let me see if I can add some code to tximeta to cover this case. I've added an argument `skipRanges` in devel branch which should allow: …

Comment: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt? by Jonathan ▴ 10

Thank you; I was indeed using `DGEList` on the count matrix, but with the multiple edits of the post I forgot to include this step. BTW, …

Comment: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt? by James W. MacDonald 67k

The other reason for doing this is because when you do `topTable(fit)`, you will automatically annotate the output data.

Comment: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt? by James W. MacDonald 67k

If you have versioned Ensembl Gene IDs, you can always use "GENEIDVERSION" for the `select` statement, or just strip off the version number…

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Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?

Answer: Limma Interaction Effect with Covariates

Comment: DESeq2 for single cell pseudobulk processing

C: Limma: how to get same output as topTable but for all the genes ?

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