DE and enrichment analysis pipeline

Question

[Pappu]

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.

[h.mon]

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

[cpad0112]

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

Answer 1

[EagleEye]

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