aop: Adverse Outcome Pathway Analysis

Share:

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.

Author
Lyle D. Burgoon <Lyle.D.Burgoon@usace.army.mil>
Date of publication
2016-12-05 18:28:47
Maintainer
Lyle D. Burgoon <Lyle.D.Burgoon@usace.army.mil>
License
CC0
Version
1.0.0

View on CRAN

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

Files in this package

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