DE and enrichment analysis pipeline · Biostar

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DE and enrichment analysis pipeline

I am wondering if there is any pipeline which runs DESeq2, EdgeR etc DE analysis and GSEA, Pathway etc enrichment and other basic analysis in one go and make the results available by some kind of shiny or other web app.

rna-seq

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updated 7.5 years ago by EagleEye

• written 7.5 years ago by Pappu

May be galaxy pipelines will do that. You can also follow workflow at http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html, http://www.sthda.com/english/wiki/rna-seq-differential-expression-work-flow-using-deseq2. If you have count matrix, this pipeline may help: https://github.com/jtlovell/deTools Pappu

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written 7.5 years ago by cpad0112

Yes, there are. A quick search led me to at least three different shiny apps. One example:

https://www.bioconductor.org/packages/release/bioc/vignettes/debrowser/inst/doc/DEBrowser.html

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written 7.5 years ago by h.mon

1 answer

Have a look at VIPER (I have not used it personally but it looks interesting).

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written 7.5 years ago by EagleEye

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