joda
This package is for version 3.9 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: 3.9
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("joda")):
Installation
To install this package, start R (version "3.6") 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 | R Script | |
| Reference Manual |
Details
| biocViews | GraphAndNetwork, Microarray, NetworkInference, Pathways, Software, StatisticalMethod |
| Version | 1.32.0 |
| 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 |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | joda_1.32.0.tar.gz |
| Windows Binary | joda_1.32.0.zip |
| Mac OS X 10.11 (El Capitan) | joda_1.32.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/joda |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/joda |
| Bioc Package Browser | https://code.bioconductor.org/browse/joda/ |
| Package Short Url | https://bioconductor.org/packages/joda/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |