LineagePulse

DOI: 10.18129/B9.bioc.LineagePulse    

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

Bioconductor version: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

HTML	R Script	LineagePulse
PDF		Reference Manual
Text		NEWS

Details

biocViews	CellBasedAssays, CellBiology, DifferentialExpression, GeneExpression, ImmunoOncology, Sequencing, SingleCell, Software, StatisticalMethod, TimeCourse
Version	1.16.0
In Bioconductor since	BioC 3.7 (R-3.5) (4.5 years)
License	Artistic-2.0
Depends
Imports	BiocParallel, circlize, compiler, ComplexHeatmap, ggplot2, gplots, grDevices, grid, knitr, Matrix, methods, RColorBrewer, SingleCellExperiment, splines, stats, SummarizedExperiment, utils
LinkingTo
Suggests
SystemRequirements
Enhances
URL
BugReports	https://github.com/YosefLab/LineagePulse/issues
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_1.16.0.tar.gz
Windows Binary	LineagePulse_1.16.0.zip (64-bit only)
macOS Binary (x86_64)	LineagePulse_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/LineagePulse
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/LineagePulse
Package Short Url	https://bioconductor.org/packages/LineagePulse/
Package Downloads Report	Download Stats