ImpulseDE

DOI: 10.18129/B9.bioc.ImpulseDE    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see ImpulseDE.

Detection of DE genes in time series data using impulse models

Bioconductor version: 3.8

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>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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")

 

PDF	R Script	ImpulseDE
PDF		Reference Manual
Text		NEWS

Details

biocViews	Software, StatisticalMethod, TimeCourse
Version	1.8.0
In Bioconductor since	BioC 3.4 (R-3.3) (2.5 years)
License	GPL-3
Depends	graphics, grDevices, stats, utils, parallel, compiler, R (>= 3.2.3)
Imports	amap, boot
LinkingTo
Suggests	longitudinal, knitr
SystemRequirements
Enhances
URL	https://github.com/YosefLab/ImpulseDE
BugReports	https://github.com/YosefLab/ImpulseDE/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	ImpulseDE_1.8.0.tar.gz
Windows Binary	ImpulseDE_1.8.0.zip
Mac OS X 10.11 (El Capitan)	ImpulseDE_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ImpulseDE
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ImpulseDE
Package Short Url	http://bioconductor.org/packages/ImpulseDE/
Package Downloads Report	Download Stats