Bioconductor TCGAWorkflow

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TCGAWorkflow

10 months ago sameerahmadguru • 0

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TCGAWorkflow

19 months ago Begin-R • 0

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TCGAWorkflow

updated 2.2 years ago by ATpoint ★ 4.5k • written 2.2 years ago by fatemehfakhari74 • 0

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TCGAbiolinks TCGAWorkflow

2.2 years ago hemangininaik09 • 0

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DifferentialExpression TCGAWorkflow

3.1 years ago Sam ▴ 10

5 results • Page 1 of 1

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Comment: What type of counts data to import for performing Isoform analysis in edgeR by ATpoint ★ 4.5k

Probably nf-core did not run with bootstrap/gibbs replicates. Check the code. See salmon docs on how to turn that on.

Comment: What type of counts data to import for performing Isoform analysis in edgeR by mohammedtoufiq91 ▴ 10

@atpoint Thank you. I did wanted to try using the `quant.sf` files from the `salmon` run by referring edgeR user guide example `4.6 Differe…

Comment: athPkgBuilder data source :missing probesets by bobihanigujjar • 0

In this article, we'll explore the demand for unbranded BJJ Gis and the benefits of choosing unbranded Gis for customization. [does anyone …

Comment: Crossover design with limma by SamGG ▴ 360

IMHO, here are the missing annotations treatmentdrug_orderDrugPlac - treatmentplacebo_orderDrugPlac, # effect of drug for the Drug…

Answer: What type of counts data to import for performing Isoform analysis in edgeR by ATpoint ★ 4.5k

You don't need any of these files. You need the `catchSalmon` function which reads `quant.sf` and the inferential (Bootstrap/Gibbs) replica…

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Comment: ANOVA like approach of edgeR

Comment: Crossover design with limma

Answer: DESeq2 normalization vs VST vs rlog

Comment: makeContrastsDream for Interaction

Answer: Limma- Print-tip loess normalisation-printer layout information does not match M

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