tradeSeq provides a flexible method for fitting regression models that can be used to find genes that are differentially expressed along one or multiple lineages in a trajectory. Based on the fitted models, it uses a variety of tests suited to answer different questions of interest, e.g. the discovery of genes for which expression is associated with pseudotime, or which are differentially expressed (in a specific region) along the trajectory. It fits a negative binomial generalized additive model (GAM) for each gene, and performs inference on the parameters of the GAM.
Package details 


Bioconductor views  Clustering DifferentialExpression GeneExpression MultipleComparison RNASeq Regression Sequencing SingleCell Software TimeCourse Transcriptomics Visualization 
Maintainer  
License  MIT + file LICENSE 
Version  1.13.06 
URL  https://statomics.github.io/tradeSeq/index.html 
Package repository  View on GitHub 
Installation 
Install the latest version of this package by entering the following in R:

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