README.md

In YosefLab/LineagePulse: Differential expression analysis and model fitting for single-cell RNA-seq data

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.

YosefLab/LineagePulse documentation built on May 6, 2019, 2:19 p.m.