statOmics/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.

Getting started

Package details

Bioconductor views Clustering DifferentialExpression GeneExpression MultipleComparison RNASeq Regression Sequencing SingleCell Software TimeCourse Transcriptomics Visualization
LicenseMIT + file LICENSE
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
statOmics/tradeSeq documentation built on Sept. 24, 2023, 9:12 p.m.