joda

DOI: 10.18129/B9.bioc.joda    

JODA algorithm for quantifying gene deregulation using knowledge

Bioconductor version: Release (3.11)

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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("joda")

 

PDF	R Script	Introduction to joda
PDF		Reference Manual

Details

biocViews	GraphAndNetwork, Microarray, NetworkInference, Pathways, Software, StatisticalMethod
Version	1.35.0
In Bioconductor since	BioC 2.8 (R-2.13) (9.5 years)
License	GPL (>= 2)
Depends	R (>= 2.0), bgmm, RBGL
Imports
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URL	http://www.bioconductor.org
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Build Report

Package Archives

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

Source Package	joda_1.35.0.tar.gz
Windows Binary	joda_1.35.0.zip
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