LineagePulse

DOI: 10.18129/B9.bioc.LineagePulse    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see LineagePulse.

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

Bioconductor version: 3.7

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("LineagePulse")

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	1.0.0
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_1.0.0.tar.gz
Windows Binary	LineagePulse_1.0.0.zip
Mac OS X 10.11 (El Capitan)	LineagePulse_1.0.0.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