How to create shiny app for deseq2 object creation

Question

[majeedmj.ict]

Hello, how we can create a shiny app to run Deseq2 ? suppose i have count table and meta table as below :

count_table

GENE	sample1	sample2	sample3	sample4	sample5
A1BG	8	8	8	7	7
A1BG-AS1	7	6	5	4	4
A1CF	6	6	6	7	6
A2M	6	6	2	7	6

meta_table

sample	type	gender
sample1	group1	Male
sample2	group1	Female
sample3	group1	Male
sample4	group2	Female
sample5	group2	Female

Deseq object created with following formula :

dds <- DESeqDataSetFromMatrix(countData = count_table,
                              colData = meta_table,
                              design= ~ type)

Question :

If User uploaded count_table and meta_table to create Deseq object . how we can create a shiny sidebar layout, where user will be able to select his choice ( either column "type" or column "gender" ) from meta_table to pass to above formula .

[Pratik]

I think Jared Andrews jared.andrews07 has created a package to do this. Check out: https://github.com/j-andrews7/iBET

[jared.andrews07]

The shinyDESeq2 function from that package will run DESeq2 from a DESeqDataSet (or you can pass it results tables directly), but you have to provide the contrast name (or it'll infer it from the design formula). It does have some nice viz and parameter tweaks available through the app, though I'll warn it's still under active development and may break/change at any time.