Bioconductor Monocle3

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SpecificClusters TrajectoryAnalysis PseudotimeAnalysis Monocle3

updated 21 months ago by mzh • 0 • written 2.5 years ago by martacrespi7 ▴ 10

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monocle3

3.2 years ago Bogdan ▴ 670

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Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Andre • 0

I edited the previous post. I meant to remove the estimateGLMRobustDisp line in the second snipper : ```` DGE_list_object <- estimateGLMR…

Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k

Sorry, I had forgotten estimateGLMDisp() produces weights as well as NB dispersions. The weights from estimatGLMRobustDisp() were intended …

Answer: Mean variance curve troubleshoot filtering by Gordon Smyth 52k

You could use `filterByExpr()`, as recommended by Law et al (2018) and in the limma and edgeR case studies. However, the main problem wi…

Comment: How do I fix an odd voom plot in a combined dataset? by Gordon Smyth 52k

You will get NA coefficients from `~Group+Batch` because the Group factor is completely confounded with the batch factor.

Comment: How do I fix an odd voom plot in a combined dataset? by 1sunmic2 • 0

Thanks for responding! I did change the code slightly: dge1 <- DGEList(counts = combined_data_counts) keep <- rowSums(cpm(dge1)…

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Comment: Comparing different method for DESEQ2

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