To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("joda")
In most cases, you don't need to download the package archive at all.
joda
|
|
|
|
|
JODA algorithm for quantifying gene deregulation using knowledge
Bioconductor version: Release (3.5)
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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("joda")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("joda")
| R Script | Introduction to joda | |
| Reference Manual |
Details
| biocViews | GraphAndNetwork, Microarray, NetworkInference, Pathways, Software, StatisticalMethod |
| Version | 1.24.0 |
| In Bioconductor since | BioC 2.8 (R-2.13) (6.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 2.0), bgmm, RBGL |
| Imports | |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
| URL | http://www.bioconductor.org |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | joda_1.24.0.tar.gz |
| Windows Binary | joda_1.24.0.zip |
| Mac OS X 10.11 (El Capitan) | joda_1.24.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/joda |
| Package Short Url | http://bioconductor.org/packages/joda/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
