Bioconductor Rmarkdown

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rmarkdown rstudio knitr

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package development bioconductor rstudio rmarkdown vignettes

7.0 years ago clarisbaby • 0

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rmarkdown package updates

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biocstyle Rmarkdown Tutorial

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rmarkdown suppressWarning warning

updated 21 months ago by Mike Smith ★ 6.6k • written 3.0 years ago by Wolfgang Huber ★ 13k

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BiocWorkflowTools rmarkdown

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BrowseSeqs DECIPHER notebook rmarkdown

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ReportingTools RNA-Seq RMarkdown

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rmarkdown knitr

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BiocWorkflowTools rmarkdown

4.5 years ago helucro ▴ 70

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Comment: Differential Expression Genes as Independent Variables by Dario Strbenac ★ 1.5k

Also, the reason why gene abundance is the dependent variable and is iterated over is that there are far more genes than there are samples …

Comment: rrvgo::calculateSimMatrix() error by Phila • 0

Thanks for sharing the solution. It helps me. [nced cloud][1] [1]: https://my-ncedcloud-login.us/

Comment: Merge Replicates vs Mixed Model by gabriel.hoffman ▴ 170

For your proteomics data, your normalization is correct. I had assumed it was RNA-seq because that is what I think about most. When using…

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

@gordonsmyth I will re-run Salmon with the --numGibbsSamples=50 option. Thank you.

Comment: Differential Expression Genes as Independent Variables by Gordon Smyth 52k

Such an analysis cannot be done in limma. Sorry, I cannot tell you how to do it or even whether it is possible.

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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

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

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