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.
Installation
To install the latest version of the R package from GitHub, please run following commands in R:
if (!require("devtools"))
install.packages("devtools")
devtools::install_github("haotian-zhuang/MUSTARD")Vignettes
Detailed vignettes are available at this website.
Citation
Please cite the following paper: Zhuang, Haotian, Xin Gai, Anru R. Zhang, Wenpin Hou, Zhicheng Ji, and Pixu Shi. “Trajectory-guided dimensionality reduction for multi-sample single-cell RNA-seq data reveals biologically relevant sample-level heterogeneity.” bioRxiv (2024): 2024-09.
Contact
Authors: Haotian Zhuang, Pixu Shi
Report bugs and provide suggestions by sending email to:
Maintainer: Haotian Zhuang (haotian.zhuang@duke.edu)
Or open a new issue on this GitHub page