DOI: 10.18129/B9.bioc.LineagePulse    

Differential expression analysis and model fitting for single-cell RNA-seq data

Bioconductor version: Release (3.8)

LineagePulse is a differential expression and expression model fitting package tailored to single-cell RNA-seq data (scRNA-seq). LineagePulse accounts for batch effects, drop-out and variable sequencing depth. One can use LineagePulse to perform longitudinal differential expression analysis across pseudotime as a continuous coordinate or between discrete groups of cells (e.g. pre-defined clusters or experimental conditions). Expression model fits can be directly extracted from LineagePulse.

Author: David S Fischer [aut, cre], Fabian Theis [ctb], Nir Yosef [ctb]

Maintainer: David S Fischer <david.fischer at>

Citation (from within R, enter citation("LineagePulse")):


To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
BiocManager::install("LineagePulse", version = "3.8")

For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script LineagePulse
PDF   Reference Manual
Text   NEWS


biocViews CellBasedAssays, CellBiology, DifferentialExpression, GeneExpression, ImmunoOncology, Sequencing, SingleCell, Software, StatisticalMethod, TimeCourse
Version 1.2.1
In Bioconductor since BioC 3.7 (R-3.5) (1 year)
License Artistic-2.0
Imports BiocParallel, circlize, compiler, ComplexHeatmap, ggplot2, gplots, grDevices, grid, knitr, Matrix, methods, RColorBrewer, SingleCellExperiment, splines, stats, SummarizedExperiment, utils
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package LineagePulse_1.2.1.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) LineagePulse_1.2.1.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats
Old Source Packages for BioC 3.8 Source Archive

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: