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biocLite("joda")
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joda
JODA algorithm for quantifying gene deregulation using knowledge
Bioconductor version: 3.0
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:
source("http://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 | 1.14.0 |
| In Bioconductor since | BioC 2.8 (R-2.13) |
| 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.
| Package Source | joda_1.14.0.tar.gz |
| Windows Binary | joda_1.14.0.zip |
| Mac OS X 10.6 (Snow Leopard) | joda_1.14.0.tgz |
| Mac OS X 10.9 (Mavericks) | joda_1.14.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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