ImpulseDE2

DOI: 10.18129/B9.bioc.ImpulseDE2    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see ImpulseDE2.

Differential expression analysis of longitudinal count data sets

Bioconductor version: 3.11

ImpulseDE2 is a differential expression algorithm for longitudinal count data sets which arise in sequencing experiments such as RNA-seq, ChIP-seq, ATAC-seq and DNaseI-seq. ImpulseDE2 is based on a negative binomial noise model with dispersion trend smoothing by DESeq2 and uses the impulse model to constrain the mean expression trajectory of each gene. The impulse model was empirically found to fit global expression changes in cells after environmental and developmental stimuli and is therefore appropriate in most cell biological scenarios. The constraint on the mean expression trajectory prevents overfitting to small expression fluctuations. Secondly, ImpulseDE2 has higher statistical testing power than generalized linear model-based differential expression algorithms which fit time as a categorial variable if more than six time points are sampled because of the fixed number of parameters.

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

Maintainer: David S Fischer <david.fischer at helmholtz-muenchen.de>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("ImpulseDE2")

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("ImpulseDE2")

 

HTML	R Script	ImpulseDE2 Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	CellBasedAssays, CellBiology, DifferentialExpression, GeneExpression, ImmunoOncology, Sequencing, Software, StatisticalMethod, TimeCourse
Version	1.11.0
In Bioconductor since	BioC 3.5 (R-3.4) (3.5 years)
License	Artistic-2.0
Depends
Imports	Biobase, BiocParallel, ComplexHeatmap, circlize, compiler, cowplot, DESeq2, ggplot2, grDevices, knitr, Matrix, methods, S4Vectors, stats, SummarizedExperiment, utils
LinkingTo
Suggests
SystemRequirements
Enhances
URL
BugReports	https://github.com/YosefLab/ImpulseDE2/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	ImpulseDE2_1.11.0.tar.gz
Windows Binary	ImpulseDE2_1.11.0.zip
macOS 10.13 (High Sierra)
Source Repository	git clone https://git.bioconductor.org/packages/ImpulseDE2
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ImpulseDE2
Package Short Url	https://bioconductor.org/packages/ImpulseDE2/
Package Downloads Report	Download Stats