joda

This package is for version 3.7 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: 3.7

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>

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

Installation

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


if (!require("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")
Introduction to joda PDF R Script
Reference Manual PDF

Details

biocViews GraphAndNetwork, Microarray, NetworkInference, Pathways, Software, StatisticalMethod
Version 1.28.0
In Bioconductor since BioC 2.8 (R-2.13) (13 years)
License GPL (>= 2)
Depends R (>= 2.0), bgmm, RBGL
Imports
System Requirements
URL http://www.bioconductor.org
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Package Archives

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

Source Package joda_1.28.0.tar.gz
Windows Binary joda_1.28.0.zip
Mac OS X 10.11 (El Capitan) joda_1.28.0.tgz
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/
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Old Source Packages for BioC 3.7 Source Archive