Bioconductor Isee

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iSEE

updated 4.2 years ago by kevin.rue ▴ 350 • written 4.2 years ago by jma1991 ▴ 70

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Network GeneNetwork iSEE

updated 4.4 years ago by Aaron Lun ★ 28k • written 4.4 years ago by Frank • 0

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iSEE SummarizedExperiment

updated 4.9 years ago by Aaron Lun ★ 28k • written 4.9 years ago by rishi.dasroy ▴ 20

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iSEE shiny summarizedExperiment News

6.0 years ago Aaron Lun ★ 28k

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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…

Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with by Devin ▴ 10

Thank you, Gordon, for your responses to all of my questions. For analysis A), in the case when a patient has either a missing timepoint or…

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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

Answer: Using TPM from tximport of Salmon output for singscore

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