The Advanced RNA-Seq plugin is backwards compatible with existing RNA-Seq TE and GE tracks. It provides powerful new statistics based on a negative binomial GLM model similar to that of edgeR; new Venn diagrams; and workflow-enabled, RNA-Seq optimized versions of existing tools.
· Multi-factorial statistics control for batch effects and support paired studies.
· Statistical results can be visualized in a genomic context as tracks, in a table view, or through the built in volcano plot.
· Heatmaps cluster samples and features simultaneously.
· PCA gives control over which principal components are shown.
· PCA and Heatmap tools overlay the visualization with known metadata about a sample.
· Venn diagrams show the differentially expressed genes shared between experimental conditions.
· All tools account for differences due to sequencing depth, removing the need to normalize input data.