Hi Vipin and Rui,

please have at the toolshed and test toolshed before developing
wrappers. For deseq2 there are already wrappers that are trying to solve
your issues and it would be nice if you could join that effort. Help
testing and contributing to it.

Ross has a cool wrapper of edgeR, DESeq2 and voom in one tool!

http://testtoolshed.g2.bx.psu.edu/view/fubar/differential_count_models

There is also that a DESeq2 single wrapper, more simplistic but
functional and with full installation of DESeq2, R3 in a reproducible
way.

http://testtoolshed.g2.bx.psu.edu/view/bgruening/deseq2

Please help Ross and me to make these wrapper rock solid!
Bjoern


> Hi All,
> 
> 
> we are making a wrapper for deseq2, and there is a step where
> control/experimental conditions
> need to be determined. For example, it would be a column like the
> following in the input file
> 
> 
> Type
> CTC
> CTC
> LM
> LM
> PT
> PT
> 
> 
> and we want the select list to contain
> 
> 
> CTC
> LM
> PT
> 
> 
> In other words, we want to filter out the 'Type' and have only
> distinct ones in the select list. We could
> make it in two steps, generate a intermediate file for this but it
> would be nice that we could directly
> retrieve the distinct types to make the list. I took a look at the
> tool config wiki, but didn't see anything
> (maybe because it was a quick scan). Does anyone have any tip on this?
> we'll really appreciate.
> 
> 
> Thanks,
> Rui
>  
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