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.
|Bioconductor views||Clustering DifferentialExpression GeneExpression MultipleComparison RNASeq Regression Sequencing SingleCell Software TimeCourse Transcriptomics Visualization|
|License||MIT + file LICENSE|
|Package repository||View on GitHub|
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