Bioconductor FilterRules

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variantannotation filterVcf readvcfasvranges filterRules

updated 9.9 years ago by Martin Morgan 25k • written 9.9 years ago by Sigve Nakken ▴ 50

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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…

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

They provide the code they used for DGE analysis in a gitlab link that can be found in the paper. In there you can find: ```` # estimate d…

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

It is not possible to use both. estimateGLMRobustDisp() estimates negative binomial dispersions for each gene, whereas glmQLFit() estimates…

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

Thank you. What is the difference between setting robust=TRUE in glmQLFit and estimateGLMRobustDisp? The paper i mentioned in the post used…

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scater/scran with TPMs from Salmon - counts?

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