tradeSeq: trajectory-based differential expression analysis for sequencing data

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

AuthorKoen Van den Berge [aut], Hector Roux de Bezieux [aut, cre] (<>), Kelly Street [ctb], Lieven Clement [ctb], Sandrine Dudoit [ctb]
Bioconductor views Clustering DifferentialExpression GeneExpression MultipleComparison RNASeq Regression Sequencing SingleCell Software TimeCourse Transcriptomics Visualization
MaintainerHector Roux de Bezieux <>
LicenseMIT + file LICENSE
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
if (!requireNamespace("BiocManager", quietly = TRUE))


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tradeSeq documentation built on Nov. 8, 2020, 7:51 p.m.