tradeSeq

trajectory-based differential expression analysis for sequencing data

Bioconductor version: 3.23 · Package version: 1.26.0

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.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("tradeSeq")