joda: JODA algorithm for quantifying gene deregulation using knowledge

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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
Date of publication
None
Maintainer
Ewa Szczurek <szczurek@molgen.mpg.de>
License
GPL (>= 2)
Version
1.22.0
URLs

View on Bioconductor

Man pages

damage
Knockout data for three regulators: ATM, RelA and p53 in two...
deregulation.p.values
Calculating deregulation p-values using resampling method.
deregulation.scores
Calculating deregulation scores.
differential.probs
Calculating probabilities of differential expression in...
regulation.scores
Calculating regulation scores.

Files in this package

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