Bioconductor Bioconducter

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HPC R Bioconducter

3.0 years ago Jitendra ▴ 10

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R Rstudio Bioconducter statistics

updated 3.1 years ago by Sean Davis 21k • written 3.2 years ago by Jitendra ▴ 10

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biomartr Bioconducter

5.7 years ago Jitendra ▴ 10

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Epigenetics R Bioconducter

2.1 years ago Jitendra ▴ 10

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Epigenetics RnBeads R Bioconducter

3.0 years ago Jitendra ▴ 10

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Comment: DESEQ2 looking at main effects while controlling for a continuous variable by James W. MacDonald 68k

The covariate is accounted for when you fit the model, so you don't need to do anything with it at the contrast step. You don't need a con…

Comment: DESEQ2 looking at main effects while controlling for a continuous variable by Lennie • 0

Thank you so much for taking the time and for the detailed explanation! I was wondering, in your numeric contrast of c(1, -1, 0,0,0), doe…

Answer: DESEQ2 looking at main effects while controlling for a continuous variable by James W. MacDonald 68k

If you use a factor effects model (with an intercept), then you will have a baseline group (the intercept), and all other coefficients exce…

Comment: Issue with DECIPHER::IdTaxa by Daniel • 0

The issue is still there and it is a real pain. ape and ade4 are used by packages like Phyloseq. There should be a way to avoid these inc…

Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with by Gordon Smyth 52k

I generally recommend `block=individual` for unbalanced designs, to recover information from incomplete blocks. I would only be disuaded fr…

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Answer: DESEQ2 looking at main effects while controlling for a continuous variable

Use of clusterProfiler : Error in testForValidKeytype(x, keytype)

Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with

Answer: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with

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