Bioconductor Trajectory analysis

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single cell trajectory analysis tscan monocle

updated 4.4 years ago by Aaron Lun ★ 28k • written 4.4 years ago by lirongrossmann ▴ 50

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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)…

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

The estimateGLMRobustDisp() function seems to have an effect on glmQLFit(), even in edgeR 4 (4.4.1). If I use estimateGLMRobustDisp(), like…

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

Here, estimateGLMRobustDisp() was used just to get the diagnostic BCV plot by plotBCV(y). The robust NB dispersions were not used for the D…

Answer: Please, I desperately need help with DESeq2. Three groups of repeated measures w by Michael Love 43k

I have to reserve my time on the support site for software related questions. I recommend working with a local statistician or someone fami…

Answer: Is it possible to work with DESeq2 where data is not properly matched for sex a by Michael Love 43k

I would probably just do the M vs M analysis. You could instead include a term for sex and have a model with all 45 samples, but the M vs M…

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