ImpulseDE

DOI: 10.18129/B9.bioc.ImpulseDE    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

Detection of DE genes in time series data using impulse models

Bioconductor version: Release (3.12)

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 "4.0") 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

PDF   Reference Manual

Details

biocViews Software, StatisticalMethod, TimeCourse
Version 1.16.0
In Bioconductor since BioC 3.4 (R-3.3) (4 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
Windows Binary
macOS 10.13 (High Sierra)
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 https://bioconductor.org/packages/ImpulseDE/
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