Bioconductor Moleculeexperiment

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JobPosting CuratedAtlasQueryR MoleculeExperiment SingleCellExperiment SpatialExperiment

19 months ago Stefano Mangiola ▴ 40

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tidySpatialExperiment SpatialExperiment MoleculeExperiment

21 months ago info ▴ 10

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MoleculeExperiment DifferentialExpression DESeq2

updated 2.1 years ago by ATpoint ★ 5.0k • written 2.1 years ago by michelafrancesconi8 • 0

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MoleculeExperiment

updated 2.4 years ago by ATpoint ★ 5.0k • written 2.4 years ago by irenekokosaikia • 0

4 results • Page 1 of 1

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Answer: Array weights in dpcDE by Gordon Smyth 53k

The uncertainty of quantification is fully accounted for in the dpcDE() analysis, including in the computation of sample weights. Your use…

Answer: lfc shrinkage estimator in DESeq2 by Michael Love 43k

Try the vignette which has a lot of information on these type of questions.

Comment: limpa analysis advice by Gordon Smyth 53k

The DPC slope is beta1. The estimated slopes for your data look pretty low, lower than I've ever used for a real dataset. Nevertheless, as …

Comment: limpa analysis advice by SamGG ▴ 360

Thanks for your feedback and for reassuring me. :-) As you suggested, I tried dpcCN() and set the slope to 0.7 in addition to the standard…

Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0

Good point, I hadn't considered the fact quantitative `time` implies a (logit-)linear response *to* time. You're correct that I haven't exp…

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A: DESeq2: Is it possible to convert read counts to expression values via TPM and r

A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen

Comment: limpa analysis advice

Answer: When to use edgeR or limma

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Popular Question to julia_mcdonough • 0