Bioconductor Scater

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runUMAP scater Matrix

updated 9 weeks ago by Hervé Pagès 16k • written 5 months ago by inzirio ▴ 10

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plotHeatmap scater

10 months ago Alina • 0

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scuttle scater

updated 8 months ago by ATpoint ★ 4.1k • written 8 months ago by Abbi Edwards • 0

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scater runPCA

updated 5 weeks ago by alan.ocallaghan ▴ 160 • written 5 weeks ago by Najla Abassi • 0

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scater

updated 3 months ago by alan.ocallaghan ▴ 160 • written 3 months ago by Dario Strbenac ★ 1.5k

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scater

updated 3 months ago by alan.ocallaghan ▴ 160 • written 3 months ago by Dario Strbenac ★ 1.5k

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scran bluster scater scuttle

updated 5 weeks ago by ATpoint ★ 4.1k • written 5 weeks ago by Dario Strbenac ★ 1.5k

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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. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…

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: Why does GSEA on edgeR results for randomized samples give highly significant p-

Answer: limma Intercept vs No-intercept models completely changing DMR results?

Answer: CombineArrays for EPIC and EPIC V2

Answer: Too many significant genes when integrating gtex and tcga

Comment: Too many significant genes when integrating gtex and tcga

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