To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ImpulseDE2")

In most cases, you don't need to download the package archive at all.

ImpulseDE2

DOI: 10.18129/B9.bioc.ImpulseDE2    

Differential expression analysis of longitudinal count data sets

Bioconductor version: Release (3.5)

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>

Citation (from within R, enter citation("ImpulseDE2")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ImpulseDE2")

Documentation

HTML R Script ImpulseDE2 Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews CellBasedAssays, CellBiology, DifferentialExpression, GeneExpression, Sequencing, Software, StatisticalMethod, TimeCourse
Version 1.0.0
In Bioconductor since BioC 3.5 (R-3.4) (< 6 months)
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
Build Report  

Package Archives

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

Package Source ImpulseDE2_1.0.0.tar.gz
Windows Binary ImpulseDE2_1.0.0.zip
Mac OS X 10.11 (El Capitan) ImpulseDE2_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ImpulseDE2
Package Short Url http://bioconductor.org/packages/ImpulseDE2/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: