joda: JODA algorithm for quantifying gene deregulation using knowledge

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).

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("joda")
AuthorEwa Szczurek
Bioconductor views GraphAndNetwork Microarray NetworkInference Pathways StatisticalMethod
Date of publicationNone
MaintainerEwa Szczurek <szczurek@molgen.mpg.de>
LicenseGPL (>= 2)
Version1.24.0
http://www.bioconductor.org

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
R
R/deregulation.p.values.R R/deregulation.scores.R R/differential.probs.R R/regulation.scores.R
build
build/vignette.rds
data
data/damage.RData
inst
inst/CITATION
inst/doc
inst/doc/JodaVignette.R
inst/doc/JodaVignette.Rnw
inst/doc/JodaVignette.pdf
man
man/damage.Rd man/deregulation.p.values.Rd man/deregulation.scores.Rd man/differential.probs.Rd man/regulation.scores.Rd
vignettes
vignettes/JodaVignette.Rnw
vignettes/figures
vignettes/figures/JODA.png

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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