LineagePulse is a differential expression algorithm for single-cell RNA-seq (scRNA-seq) data. Its main application is differential expression analysis across pseudotemporal orderings (developmental trajectories) of scRNA-seq data. LineagePulse can also be used for group-wise differential expression tests. As LineagePulse is based on model fitting, it can also be used for batch correction and gene expression trajectory estimation only.
Clone the GitHub LineagePulse repository first into you local target directory and then install the package via "R CMD INSTALL .".
View the vignette (.html) in your browser by double clicking on "vignettes/LineagePulse_Tutorial.Rmd".
LineagePulse is parallelised with BiocParallel. If BiocParallel does not start any processes during the model estimation, add options(bphost="localhost") into your R script before the first call to any LineagePulse function.