ImpulseDE2
This package is for version 3.11 of Bioconductor. This package has been removed from Bioconductor. For the last 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>
citation("ImpulseDE2")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("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")| ImpulseDE2 Vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CellBasedAssays, CellBiology, DifferentialExpression, GeneExpression, ImmunoOncology, Sequencing, Software, StatisticalMethod, TimeCourse |
| Version | 1.11.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (7 years) |
| License | Artistic-2.0 |
| Depends | |
| Imports | Biobase, BiocParallel, ComplexHeatmap, circlize, compiler, cowplot, DESeq2, ggplot2, grDevices, knitr, Matrix, methods, S4Vectors, stats, SummarizedExperiment, utils |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/YosefLab/ImpulseDE2/issues |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/ImpulseDE2/ |
| Package Short Url | https://bioconductor.org/packages/ImpulseDE2/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.11 | Source Archive |