Bioconductor Sushi

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sushi

updated 8.7 years ago by Steve Lianoglou ★ 13k • written 8.7 years ago by Bogdan ▴ 670

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R sushi

updated 8.3 years ago by dphansti ▴ 10 • written 8.3 years ago by javier.mendoza • 0

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sushi plotBed

updated 8.1 years ago by dphansti ▴ 10 • written 8.3 years ago by Dimitris Polychronopoulos ▴ 80

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Sushi

updated 8.1 years ago by dphansti ▴ 10 • written 8.1 years ago by Till ▴ 30

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sushi plotBed data.frame

8.0 years ago waqasnayab • 0

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sushi

7.6 years ago snamjoshi87 ▴ 40

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729

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sushi plotGenes

6.3 years ago portia.mcghan • 0

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sushi bed

5.6 years ago maltethodberg ▴ 180

8 results • Page 1 of 1

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Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k

This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…

Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0

Thank you Tim, this is a great help in getting me started!

Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k

Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…

Answer: Too many significant genes when integrating gtex and tcga by James W. MacDonald 65k

See `?results`, in particular the lfcThreshold argument.

Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k

You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…

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Answer: CombineArrays for EPIC and EPIC V2

Answer: Too many significant genes when integrating gtex and tcga

Comment: Too many significant genes when integrating gtex and tcga

A: Print Differentially Expressed Exons From Dexseq Results

stuck on unimplemented type 'list' in 'EncodeElement'

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