tradeSeq

tradeSeq fits regression models to identify genes that are differentially expressed along one or multiple lineages in a trajectory.

Key Features:

• Negative binomial generalized additive model (GAM) fitting: Fits a negative binomial GAM for each gene and performs inference on the parameters of the GAM.
• Flexible differential expression testing: Uses a variety of tests suited to answer different questions of interest based on the fitted models.
• Pseudotime association testing: Discovers genes for which expression is associated with pseudotime.
• Region-specific differential expression: Identifies genes that are differentially expressed in a specific region along the trajectory.

Scientific Applications:

• Trajectory-based differential expression analysis: Finds genes that are differentially expressed along one or multiple lineages in a trajectory from sequencing data.

Methodology:

tradeSeq fits a negative binomial generalized additive model (GAM) for each gene and performs inference on the parameters of the GAM.