Bioconductor Rna-seq

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deseq2 edgeR rna-seq

updated 16 days ago by Elizabeth • 0 • written 8.8 years ago by gthm ▴ 30

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rna-seq edgeR

updated 14 days ago by Gordon Smyth 50k • written 26 days ago by Netanel • 0

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RNA-seq DESeq2

updated 1 day ago by Michael Love 41k • written 1 day ago by Reza • 0

3 results • Page 1 of 1

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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0

Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …

Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k

Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…

Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k

I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …

Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k

It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …

Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k

This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…

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Answer: CombineArrays for EPIC and EPIC V2

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