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LineagePulse

This is the development version of LineagePulse; for the stable release version, see LineagePulse.

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

Bioconductor version: Development (3.18)

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 helmholtz-muenchen.de>

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

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("LineagePulse")

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

Documentation

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

browseVignettes("LineagePulse")
LineagePulse HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews CellBasedAssays, CellBiology, DifferentialExpression, GeneExpression, ImmunoOncology, Sequencing, SingleCell, Software, StatisticalMethod, TimeCourse
Version 1.21.0
In Bioconductor since BioC 3.7 (R-3.5) (5.5 years)
License Artistic-2.0
Depends
Imports BiocParallel, circlize, compiler, ComplexHeatmap, ggplot2, gplots, grDevices, grid, knitr, Matrix, methods, RColorBrewer, SingleCellExperiment, splines, stats, SummarizedExperiment, utils
Linking To
Suggests
System Requirements
Enhances
URL
Bug Reports https://github.com/YosefLab/LineagePulse/issues
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Package Archives

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

Source Package LineagePulse_1.21.0.tar.gz
Windows Binary LineagePulse_1.21.0.zip
macOS Binary (x86_64) LineagePulse_1.21.0.tgz
macOS Binary (arm64) LineagePulse_1.21.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/LineagePulse
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/LineagePulse
Bioc Package Browser https://code.bioconductor.org/browse/LineagePulse/
Package Short Url https://bioconductor.org/packages/LineagePulse/
Package Downloads Report Download Stats