zenith

zenith performs gene set analysis on differential expression results from linear (mixed) modeling with dream by accounting for correlation between gene expression traits.

Key Features:

• camera method implementation: zenith implements the camera method from the limma package proposed by Wu and Smyth (2012).
• Linear mixed model compatibility: zenith extends camera to be compatible with linear mixed models implemented in variancePartition::dream().
• Correlation-aware analysis: zenith considers the correlation between gene expression traits during gene set analysis.

Scientific Applications:

• Differential expression downstream analysis: zenith performs gene set analysis following differential expression using linear (mixed) modeling with dream.

Methodology:

zenith extends the camera method from the limma package to be compatible with linear mixed models implemented in variancePartition::dream().