joda

DOI: 10.18129/B9.bioc.joda    

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

This package is for version 3.12 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see joda.

JODA algorithm for quantifying gene deregulation using knowledge

Bioconductor version: 3.12

Package 'joda' implements three steps of an algorithm called JODA. The algorithm computes gene deregulation scores. For each gene, its deregulation score reflects how strongly an effect of a certain regulator's perturbation on this gene differs between two different cell populations. The algorithm utilizes regulator knockdown expression data as well as knowledge about signaling pathways in which the regulators are involved (formalized in a simple matrix model).

Author: Ewa Szczurek

Maintainer: Ewa Szczurek <szczurek at molgen.mpg.de>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("joda")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	GraphAndNetwork, Microarray, NetworkInference, Pathways, Software, StatisticalMethod
Version	1.38.0
In Bioconductor since	BioC 2.8 (R-2.13) (10 years)
License	GPL (>= 2)
Depends	R (>= 2.0), bgmm, RBGL
Imports
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URL	http://www.bioconductor.org
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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/joda
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/joda
Package Short Url	https://bioconductor.org/packages/joda/
Package Downloads Report	Download Stats