aop: Adverse Outcome Pathway Analysis
Version 1.0.0

Provides tools for analyzing adverse outcome pathways (AOPs) for pharmacological and toxicological research. Functionality includes the ability to perform causal network analysis of networks developed in and exported from Cytoscape or existing as R graph objects, and identifying the point of departure/screening/risk value from concentration- response data.

AuthorLyle D. Burgoon <Lyle.D.Burgoon@usace.army.mil>
Date of publication2016-12-05 18:28:47
MaintainerLyle D. Burgoon <Lyle.D.Burgoon@usace.army.mil>
LicenseCC0
Version1.0.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("aop")

Getting started

README.md
AOP Vignette
Concentration-Response Analysis to Identify a Chemical's Point of Departure Using the AOP Package

Popular man pages

bootstrap_metaregression: Perform Bootstrap Metaregression
convert_aop_to_graph: Convert AOP to Graph
convert_cytoscape_to_aop: Convert Cytoscape Graph to an AOP
internal_model_fits: An internal function for calculating interpolation values.
plot_metaregression_spaghetti_plot: Make a spaghetti plot for the metaregression results
plot_slope_analysis: Plot the median slope
slope_pod_analysis: Slope-based POD analysis
See all...

All man pages Function index File listing

Man pages

aop_backdoor: Backdoor Causal Network Analysis for AOPs
aop_cytoscape-class: aop_cytoscape class
aop_cytoscape-methods: Get Node Name from ID
bmr-class: bmr class
bootstrap_metaregression: Perform Bootstrap Metaregression
calculate_confidence_and_median: Calculate the confidence envelope and the median for the...
convert_aop_to_graph: Convert AOP to Graph
convert_cytoscape_to_aop: Convert Cytoscape Graph to an AOP
internal_model_fits: An internal function for calculating interpolation values.
oxybenzone: High Throughput Screening Data (Tox21) for Assessing the...
plot_metaregression_confidence_envelope: Plot the metaregression confidence envelope and median...
plot_metaregression_spaghetti_plot: Make a spaghetti plot for the metaregression results
plot_slope_analysis: Plot the median slope
pod_envelope_analysis: This function calculates the chemical's point of departure.
pod_slope_analysis: This is intended as an internal function to facilitate the...
slope_pod_analysis: Slope-based POD analysis

Functions

aop_backdoor Man page Source code
aop_cytoscape Man page
aop_cytoscape-class Man page
bmr Man page
bmr-class Man page
bootstrap_metaregression Man page Source code
calculate_confidence_and_median Man page Source code
convert_aop_to_graph Man page Source code
convert_cytoscape_to_aop Man page Source code
getAOPNodeName Man page
getAOPNodeName,aop_cytoscape-method Man page
internal_model_fits Man page Source code
oxybenzone Man page
plot_metaregression_confidence_envelope Man page Source code
plot_metaregression_spaghetti_plot Man page Source code
plot_slope_analysis Man page Source code
pod_envelope_analysis Man page Source code
pod_slope_analysis Man page Source code
slope_pod_analysis Man page Source code

Files

inst
inst/NEWS
inst/extdata
inst/extdata/steatosis_aop.png
inst/extdata/steatosis_aop_json.cyjs
inst/doc
inst/doc/aop.Rmd
inst/doc/concentration-response_analysis.R
inst/doc/aop.R
inst/doc/concentration-response_analysis.html
inst/doc/aop.html
inst/doc/concentration-response_analysis.Rmd
inst/unitTests
inst/unitTests/test_functions.R
tests
tests/runTests.R
NAMESPACE
data
data/oxybenzone.rda
R
R/pod_analysis.R
R/aop_graph_analysis.R
R/aopCytoscape_Class.R
R/bmr_Class.R
R/aop_cytoscape_methods.R
vignettes
vignettes/aop.Rmd
vignettes/concentration-response_analysis.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/internal_model_fits.Rd
man/pod_envelope_analysis.Rd
man/convert_aop_to_graph.Rd
man/pod_slope_analysis.Rd
man/bmr-class.Rd
man/aop_backdoor.Rd
man/aop_cytoscape-class.Rd
man/oxybenzone.Rd
man/calculate_confidence_and_median.Rd
man/plot_metaregression_spaghetti_plot.Rd
man/aop_cytoscape-methods.Rd
man/slope_pod_analysis.Rd
man/convert_cytoscape_to_aop.Rd
man/bootstrap_metaregression.Rd
man/plot_slope_analysis.Rd
man/plot_metaregression_confidence_envelope.Rd
aop documentation built on May 20, 2017, 12:49 a.m.

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Please suggest features or report bugs in the GitHub issue tracker.

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