## LineagePulse ## ### Differential expression analysis and model fitting for single-cell RNA-seq data in pseudotime ### 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. ### INSTALLATION Clone the GitHub LineagePulse repository first into you local target directory and then install the package via "R CMD INSTALL .". ### VIGNETTE View the vignette (.html) in your browser by double clicking on "vignettes/LineagePulse_Tutorial.Rmd". ### Problems with BiocParallel: 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.