MetaR: 1.9.0 April 15 2016

Add normalized table output for Limma Voom statement (previously normalized counts were written to the adjusted table, but this table was only available if you had more than one factor in the model). This change makes it possible to get normalized expression data in the more common situation of a model with one factor. Add the ability to choose a group to identify the column that contains the names of the genes to show on a heatmap. Migration script will set this new annotation to the default ID group. Add support to generate MA Plots as well as UpSet plots Add support for Sleuth. You can now read Kallisto results directly with MetaR and call transcripts differentially expressed with Sleuth. The sleuth statement integrates with the Table annotation capabilities of MetaR and supports both Wald and likelihood ratio tests. Improve editing of R code, especially when calling functions. Change the keystroke to open the table viewer. It was bound to Shift T, which prevented users from typing an uppercase T in the table name. Code: started using the org.campagnelab.metar.R language to write generators for MetaR statements. Added metar.R.inspect to help with development of generators using the R language (this language is the equivalent of the metar.inspect language which was designed to be used with TextOutput in generators). *Code: Add IListenOnPort ConceptInterface and use it when ports need to be exposed by docker when executing a script