How to create shiny app for deseq2 object creation
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10 months ago
majeedmj.ict ▴ 20

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 .

shiny deseq2 • 511 views
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I think Jared Andrews jared.andrews07 has created a package to do this. Check out: https://github.com/j-andrews7/iBET

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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.

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