LineagePulse

DOI: 10.18129/B9.bioc.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 (3.9)

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 "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("LineagePulse", version = "3.9")

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, Sequencing, SingleCell, Software, StatisticalMethod, TimeCourse
Version 1.3.0
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_1.3.0.tar.gz
Windows Binary LineagePulse_1.3.0.zip
Mac OS X 10.11 (El Capitan) LineagePulse_1.3.0.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 http://bioconductor.org/packages/LineagePulse/
Package Downloads Report Download Stats

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