Trajectory-guided dimensionality reduction for multi-sample single-cell RNA-seq data reveals biologically relevant sample-level heterogeneity

The R package MUSTARD (MUlti-Sample Trajectory-Assisted Reduction of Dimensions) implements a trajectory-guided dimensionality reduction method for multi-sample scRNA-seq data. This all-in-one decomposition reveals major gene expression variation patterns along the trajectory and across multiple samples simultaneously, providing opportunities to discover sample endotypes and associated genes.