Bioconductor Designformula

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designformula DESeq2

updated 17 months ago by swbarnes2 ★ 1.4k • written 17 months ago by Grace.Ciabattoni • 0

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DEGseq DESeq2 Designformula

updated 3.6 years ago by swbarnes2 ★ 1.4k • written 3.6 years ago by Nicolò • 0

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DESeq2 matrixnotfullrank Designformula DEseq2

3.8 years ago Nicolò • 0

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Answer: What type of counts data to import for performing Isoform analysis in edgeR by Gordon Smyth 52k

I haven't used nf-core but, from browsing through their documentation, they didn't seem to have any pipeline for differential transcript ex…

Comment: What type of counts data to import for performing Isoform analysis in edgeR by Gordon Smyth 52k

The poster needs to run Salmon with `--numGibbsSamples=50`. I suspect that nf-core just won't do that, so Salmon needs to be run directly.

Comment: What type of counts data to import for performing Isoform analysis in edgeR by ATpoint ★ 4.6k

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 …

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Transcript-level differential expression using DESeq2

Comment: What type of counts data to import for performing Isoform analysis in edgeR

Answer: What type of counts data to import for performing Isoform analysis in edgeR

Comment: ANOVA like approach of edgeR

Comment: Crossover design with limma

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