simPATHy: A Method for Simulating Data from Perturbed Biological Pathways

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Simulate data from a Gaussian graphical model or a Gaussian Bayesian network in two conditions. Given a covariance matrix of a reference condition simulate plausible dysregulations.

Author
Elisa Salviato [aut, cre], Vera Djordjilovic [aut], Chiara Romualdi [aut], Monica Chiogna [aut]
Date of publication
2016-09-21 07:27:43
Maintainer
Elisa Salviato <elisa.salviato.88@gmail.com>
License
AGPL-3
Version
0.2

View on CRAN

Man pages

chimera
Chimera data
easyLookDys
Dysregulation summary
easyLookShiny
Visual dysregulation summary
fitSgraph
Estimate covariance matrix of a graphical model
generatePath
Find one path in a graph
getPathShiny
Choose a path in a graph from an interactive shiny app
graphNELD3-shiny
Shiny bindings for plotGraphNELD3
makePositiveDefinite
Positive definite matrix
plotCorGraph
Plot correlation or partial correlation matrix
plotGraphNELD3
Dynamic plot of a graph
simPATHy
Simulate data from a graphical model
SMLEdecomposable
Local Maximum Likelihood Estimation

Files in this package

simPATHy
simPATHy/inst
simPATHy/inst/htmlwidgets
simPATHy/inst/htmlwidgets/graphNELD3.js
simPATHy/inst/htmlwidgets/lib
simPATHy/inst/htmlwidgets/lib/d3-3.5.2
simPATHy/inst/htmlwidgets/lib/d3-3.5.2/d3.min.js
simPATHy/inst/htmlwidgets/graphNELD3.yaml
simPATHy/inst/doc
simPATHy/inst/doc/simPATHy.html
simPATHy/inst/doc/simPATHy.Rmd
simPATHy/inst/doc/simPATHy.R
simPATHy/NAMESPACE
simPATHy/data
simPATHy/data/datalist
simPATHy/data/chimera.rda
simPATHy/R
simPATHy/R/graphic_function.R
simPATHy/R/graphNELD3.R
simPATHy/R/main_function.R
simPATHy/R/secondary_function.R
simPATHy/vignettes
simPATHy/vignettes/images
simPATHy/vignettes/images/getPathShiny.png
simPATHy/vignettes/images/easyLookShiny.png
simPATHy/vignettes/images/plotGraphNELD3.png
simPATHy/vignettes/simPATHy.Rmd
simPATHy/vignettes/biblio.bib
simPATHy/MD5
simPATHy/build
simPATHy/build/vignette.rds
simPATHy/DESCRIPTION
simPATHy/man
simPATHy/man/simPATHy.Rd
simPATHy/man/getPathShiny.Rd
simPATHy/man/makePositiveDefinite.Rd
simPATHy/man/plotCorGraph.Rd
simPATHy/man/easyLookShiny.Rd
simPATHy/man/generatePath.Rd
simPATHy/man/graphNELD3-shiny.Rd
simPATHy/man/chimera.Rd
simPATHy/man/easyLookDys.Rd
simPATHy/man/SMLEdecomposable.Rd
simPATHy/man/fitSgraph.Rd
simPATHy/man/plotGraphNELD3.Rd