• Manuals

Browse the manual

• Introduction to the Advanced RNA-Seq plugin
  • Input data and normalization
    • Normalization
    • Metadata
  • PCA for RNA-Seq
    • Principal component analysis plot (2D)
    • Principal component analysis plot (3D)
  • Differential Expression for RNA-Seq
    • The statistical model
    • Output of the Differential Expression for RNA-Seqtool
    • Statistical comparison tracks
    • The volcano plot
  • Create Heat Map for RNA-Seq
    • Clustering of features and samples
    • The heat map view
  • Create Expression Browser
    • The expression browser
  • Create Venn Diagram for RNA-Seq
    • Venn diagram table view
• Installation of the Advanced RNA-Seq plugin
• Uninstall
• Bibliography

Metadata

The new statistical analysis and visualization tools make extensive use of the metadata system. For example, metadata are required when defining the experimental design in the Differential Expression for RNA-Seq tool, and can be used to add extra layers of insight in the Create Heat Map and PCA for RNA-Seq tools.

To get the most out of these tools we recommend that all input expression tracks have associated metadata, as shown in figure 1.2. For information about how to use and setup metadata, please see

Figure 1.2: An example of expression tracks with associated metadata.

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