Bioconductor AUCell

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AUCell AUcell

9 weeks ago • updated 5 weeks ago Lucy ▴ 60

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AUCell

updated 11 months ago by ATpoint ★ 3.4k • written 11 months ago by Lucy ▴ 60

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RcisTarget aucell SCENIC

updated 5.3 years ago by Martin Morgan 25k • written 5.3 years ago by jka8119 ▴ 10

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AUCell SCENIC

updated 5.3 years ago by sara.aibar ▴ 10 • written 5.3 years ago by Xingyu • 0

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Comment: Phenotype effect - building a contrast matrix - grouping vs interaction by Gordon Smyth 48k

I am telling you that `LS_B.vs.NL_B` is completely uninteresting. You need instead to examine `LS_Y.vs.NL_Y` and `LS_N.vs.NL_N` separately.

Answer: Batch correction and repeated measures by Gordon Smyth 48k

You should just do a standard limma analysis as recommended in the previous posts. ``` design <- model.matrix(~0 + Sample.Type + batch) i <…

Comment: DESeq2, results(dds, name = <reference>) interpretation results by Rockbar • 0

When I apply the model.matrix approach for getting the contrasts, the code > mod_mat <- model.matrix(design(dds), colData(dds)) > CondA.t…

Comment: DESeq2, results(dds, name = <reference>) interpretation results by Rockbar • 0

Yes, I agree, the correct contrast setting is quite challenging. The vignette says >contrast: a list of 2 character vectors: the names of…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k

Advantage and disadvantage depends on the aim, what you plan to do with them (testing, plots, etc.). lengthScaledTPM puts back *in* the ge…

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Comment: Phenotype effect - building a contrast matrix - grouping vs interaction

Answer: Batch correction and repeated measures

Answer: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?

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Scholar to James W. MacDonald 63k