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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