ImpulseDE

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see ImpulseDE2.

Detection of DE genes in time series data using impulse models


Bioconductor version: 3.9

ImpulseDE is suited to capture single impulse-like patterns in high throughput time series datasets. By fitting a representative impulse model to each gene, it reports differentially expressed genes whether across time points in a single experiment or between two time courses from two experiments. To optimize the running time, the code makes use of clustering steps and multi-threading.

Author: Jil Sander [aut, cre], Nir Yosef [aut]

Maintainer: Jil Sander <jil.sander at uni-bonn.de>, Nir Yosef <niryosef at berkeley.edu>

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

Installation

To install this package, start R (version "3.6") and enter:


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

BiocManager::install("ImpulseDE")

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("ImpulseDE")
ImpulseDE PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Software, StatisticalMethod, TimeCourse
Version 1.10.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License GPL-3
Depends graphics, grDevices, stats, utils, parallel, compiler, R (>= 3.2.3)
Imports amap, boot
System Requirements
URL https://github.com/YosefLab/ImpulseDE
Bug Reports https://github.com/YosefLab/ImpulseDE/issues
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Suggests longitudinal, knitr
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Package Archives

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

Source Package ImpulseDE_1.10.0.tar.gz
Windows Binary ImpulseDE_1.10.0.zip
Mac OS X 10.11 (El Capitan) ImpulseDE_1.10.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ImpulseDE
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ImpulseDE
Bioc Package Browser https://code.bioconductor.org/browse/ImpulseDE/
Package Short Url https://bioconductor.org/packages/ImpulseDE/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive