Bioconductor MetaMS

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XCMS metaMS

updated 4.5 years ago by ron.wehrens ▴ 20 • written 4.5 years ago by julien.kermorvant ▴ 30

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metams

5.3 years ago ryan.high • 0

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metaMS

updated 5.3 years ago by ron.wehrens ▴ 20 • written 5.3 years ago by f.f.vandenberg • 0

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metaMS xcmx CAMERA

updated 8.2 years ago by ron.wehrens ▴ 20 • written 8.2 years ago by lucie.conchou • 0

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metaMS xcms GC-MS metabolomics volatile organic compounds

updated 8.5 years ago by ron.wehrens ▴ 20 • written 8.5 years ago by lucie.conchou • 0

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xcms metaMS MSeasy r

updated 9.2 years ago by peer.karmaus • 0 • written 9.2 years ago by Nemo ▴ 80

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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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