We have just released MetaR 1.8.0 (available from the JetBrains MPS plugin repository, see installation instructions). This release includes a number of new features:

  • Support to generate UpSet plots to look at intersection of gene lists/and or table subsets:

UpSet_in_MetaR

  • Added the ability to create annotated MA Plots (Thanks go to Kevin Hadi for the R code this generates to):

MA_Plot_in_MetaR

  • New 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.

Sleuth_MetaR

Once configured, this is what a Sleuth analysis looks like in MetaR:

ConfiuguredSleuthTutorial

  • 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.
  • Improve editing of R code, especially when calling functions.

The documentation has been updated to describe these new features. See the index heading “New in MetaR 1.8” to locate the updates.