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Showing posts from June, 2019

DEE2 project update June 2019

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It has been wonderful to be getting great feedback on DEE2, ways it can be improved and directions for future development of open omics data. Here I'll summarise some of these points.
Recent developmentsiDEP integration. The iDEP service has provided DEE2 counts on it's R Shiny powered page which makes it very easy to download and analyse DEE2 data using the iDEP bioinformatics in the browser platform: http://bioinformatics.sdstate.edu/reads/
Degust integration. When using DEE2 in the browser you can now choose to send count matrices to Degust for differential analysis. You can send either the STAR gene counts, Kallisto Tx counts or Kallisto Tx counts aggregated to gene counts (recommended). Many thanks to David Powell's team at Monash especially Andrew Perry for working with me on adding this feature.
The R package getDEE2 now works for Windows systems. This required a modification to the download.file() options to account for default behaviour on these OSs. Thanks to Steve…