Bioconductor BiocSingular

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BiocSingular zellkonverter batchelor

updated 3.9 years ago by luke.zappia ▴ 50 • written 3.9 years ago by jma1991 ▴ 70

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scater BiocSingular DelayedArray

updated 5.5 years ago by Aaron Lun ★ 28k • written 5.5 years ago by kevin.rue ▴ 350

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Comment: Crossover design with limma by SamGG ▴ 360

IMHO, here are the missing annotations treatmentdrug_orderDrugPlac - treatmentplacebo_orderDrugPlac, # effect of drug for the Drug…

Answer: What type of counts data to import for performing Isoform analysis in edgeR by ATpoint ★ 4.5k

You don't need any of these files. You need the `catchSalmon` function which reads `quant.sf` and the inferential (Bootstrap/Gibbs) replica…

Comment: makeContrastsDream for Interaction by abadgerw • 0

Thank you! I will try this out.

Comment: Merge Replicates vs Mixed Model by abadgerw • 0

Thanks, @gabrielhoffman The data is actually proteomics so it is intensity data which is why I did not use voom but rather ran ebayes wi…

Comment: ANOVA like approach of edgeR by Gordon Smyth 52k

To identify common upregulated or downregulated genes, you would need to test for media condition contrasts for each cell type separately, …

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Comment: Crossover design with limma

Answer: DESeq2 normalization vs VST vs rlog

Comment: makeContrastsDream for Interaction

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