The tools from the Advanced RNA-Seq plugin have been moved into CLC Genomics Workbench and Biomedical Genomics Workbench in March 2017. They can be found in the new "RNA-Seq Analysis" section of the toolbox.
The new tools are:
- PCA for RNA-Seq clusters samples in 2D or 3D. Known metadata about each sample is added as an overlay.
- Differential Expression for RNA-Seq uses multi-factorial statistics based on a negative binomial GLM. The tool supports paired designs and can control for batch effects.
- Create Heat Map for RNA-Seq simultaneously clusters samples and features. Known metadata about each sample is added as an overlay.
- Create Expression Browser allows expression values, statistical results, and gene annotations to be viewed together.
- Create Venn Diagram for RNA-Seq shows differentially expressed genes shared between experimental conditions.
The Advanced RNA-seq tools require RNA-Seq input data in the form of Expression Tracks, unlike the tools included in the "Microarray and Small RNA" folder that also support microarray data or Experiment objects.
In addition, the tools from the RNA-Seq folder automatically account for differences due to sequencing depth, removing the need to normalize input data.
Finally, the statistical analysis and visualization tools of the RNA-Seq folder make extensive use of the metadata system.