OncoSimulR: Forward Genetic Simulation of Cancer Progression with Epistasis

Functions for forward population genetic simulation in asexual populations, with special focus on cancer progression. Fitness can be an arbitrary function of genetic interactions between multiple genes or modules of genes, including epistasis, order restrictions in mutation accumulation, and order effects. Mutation rates can differ between genes, and we can include mutator/antimutator genes (to model mutator phenotypes). Simulations use continuous-time models and can include driver and passenger genes and modules. Also included are functions for: simulating random DAGs of the type found in Oncogenetic Tress, Conjunctive Bayesian Networks, and other tumor progression models; plotting and sampling from single or multiple realizations of the simulations, including single-cell sampling; plotting the parent-child relationships of the clones; generating random fitness landscapes (Rough Mount Fuji, House of Cards, and additive models) and plotting them.

AuthorRamon Diaz-Uriarte [aut, cre], Mark Taylor [ctb]
Date of publicationNone
MaintainerRamon Diaz-Uriarte <rdiaz02@gmail.com>
LicenseGPL (>= 3)
Version2.4.0
https://github.com/rdiaz02/OncoSimul, https://popmodels.cancercontrol.cancer.gov/gsr/packages/oncosimulr/

View on Bioconductor

Files in this package

OncoSimulR/DESCRIPTION
OncoSimulR/NAMESPACE
OncoSimulR/R
OncoSimulR/R/OncoSimulR.R OncoSimulR/R/RcppExports.R OncoSimulR/R/conversion-helpers.R OncoSimulR/R/fitness_landscape_utils.R OncoSimulR/R/from_genotype_utils.R OncoSimulR/R/generate-random-trees.R OncoSimulR/R/mutator.R OncoSimulR/R/new-restrict.R OncoSimulR/R/rfitness.R OncoSimulR/R/stacked-plots.R
OncoSimulR/build
OncoSimulR/build/vignette.rds
OncoSimulR/data
OncoSimulR/data/ex_missing_drivers_b11.RData
OncoSimulR/data/ex_missing_drivers_b12.RData
OncoSimulR/data/examplePosets.RData
OncoSimulR/data/examplesFitnessEffects.RData
OncoSimulR/data/mcfLs.RData
OncoSimulR/inst
OncoSimulR/inst/CITATION
OncoSimulR/inst/NEWS
OncoSimulR/inst/doc
OncoSimulR/inst/doc/OncoSimulR.R
OncoSimulR/inst/doc/OncoSimulR.Rmd
OncoSimulR/inst/doc/OncoSimulR.html
OncoSimulR/inst/miscell
OncoSimulR/inst/miscell/example-binom-problems.cpp
OncoSimulR/man
OncoSimulR/man/OncoSimulWide2Long.Rd OncoSimulR/man/allFitnessEffects.Rd OncoSimulR/man/evalAllGenotypes.Rd OncoSimulR/man/example-missing-drivers.Rd OncoSimulR/man/examplePosets.Rd OncoSimulR/man/examplesFitnessEffects.Rd OncoSimulR/man/mcfLs.Rd OncoSimulR/man/oncoSimulIndiv.Rd OncoSimulR/man/plot.fitnessEffects.Rd OncoSimulR/man/plot.oncosimul.Rd OncoSimulR/man/plotClonePhylog.Rd OncoSimulR/man/plotFitnessLandscape.Rd OncoSimulR/man/plotPoset.Rd OncoSimulR/man/poset.Rd OncoSimulR/man/rfitness.Rd OncoSimulR/man/samplePop.Rd OncoSimulR/man/simOGraph.Rd OncoSimulR/man/to_Magellan.Rd
OncoSimulR/src
OncoSimulR/src/BNB_nr.cpp
OncoSimulR/src/BNB_v1.cpp
OncoSimulR/src/Makevars
OncoSimulR/src/Makevars.win
OncoSimulR/src/OncoSimulR_init.c
OncoSimulR/src/RcppExports.cpp
OncoSimulR/src/bnb_common.cpp
OncoSimulR/src/bnb_common.h
OncoSimulR/src/common_classes.h
OncoSimulR/src/debug_common.h
OncoSimulR/src/new_restrict.cpp
OncoSimulR/src/new_restrict.h
OncoSimulR/src/new_restrict_former_print_utils.cpp
OncoSimulR/tests
OncoSimulR/tests/README_names.txt
OncoSimulR/tests/manual
OncoSimulR/tests/manual/README.txt
OncoSimulR/tests/manual/test.Z-driverCounts-long.R
OncoSimulR/tests/manual/test.Z-sample-only-last-long.R
OncoSimulR/tests/manual/test.Z-warning-mutPropGrowth-long.R
OncoSimulR/tests/manual/test.driverCounts-long.R
OncoSimulR/tests/manual/test.exercise-plotting-code-long.R
OncoSimulR/tests/manual/test.fitness-preds-long.R
OncoSimulR/tests/manual/test.mutPropGrowth-long.R
OncoSimulR/tests/manual/test.mutator-long.R
OncoSimulR/tests/manual/test.mutator-oncoSimulSample-long.R
OncoSimulR/tests/manual/test.oncoSimulSample-limits-long.R
OncoSimulR/tests/manual/test.per-gene-mutation-rates-long.R
OncoSimulR/tests/manual/test.poset-transformations-long.R
OncoSimulR/tests/manual/test.sample-prob-long.R
OncoSimulR/tests/manual/test.simuls-run-examples-long.R
OncoSimulR/tests/manual/test.warning-mutPropGrowth-long.R
OncoSimulR/tests/testthat
OncoSimulR/tests/testthat.R
OncoSimulR/tests/testthat/test.Z-all-fitness.R
OncoSimulR/tests/testthat/test.Z-driverCounts.R
OncoSimulR/tests/testthat/test.Z-mutator.R
OncoSimulR/tests/testthat/test.Z-oncoSimulIndiv.R
OncoSimulR/tests/testthat/test.Z-rfitness-landscape.R
OncoSimulR/tests/testthat/test.Z-sample-only-last.R
OncoSimulR/tests/testthat/test.Z-total-present-drivers.R
OncoSimulR/tests/testthat/test.all-fitness.R
OncoSimulR/tests/testthat/test.driverCounts.R
OncoSimulR/tests/testthat/test.epist-order-modules.R
OncoSimulR/tests/testthat/test.exercise-plotting-code.R
OncoSimulR/tests/testthat/test.exercise-rfitness.R
OncoSimulR/tests/testthat/test.exercise-to-Magellan.R
OncoSimulR/tests/testthat/test.fitness-preds.R
OncoSimulR/tests/testthat/test.genotFitness.R
OncoSimulR/tests/testthat/test.init-mutant.R
OncoSimulR/tests/testthat/test.modules-root-no-root.R
OncoSimulR/tests/testthat/test.mutPropGrowth.R
OncoSimulR/tests/testthat/test.mutator-oncoSimulSample.R
OncoSimulR/tests/testthat/test.mutator.R
OncoSimulR/tests/testthat/test.oncoSimulIndiv-miscell.R
OncoSimulR/tests/testthat/test.oncoSimulSample-failures.R
OncoSimulR/tests/testthat/test.oncoSimulSample-limits.R
OncoSimulR/tests/testthat/test.per-gene-mutation-rates.R
OncoSimulR/tests/testthat/test.plotFitnessLandscape.R
OncoSimulR/tests/testthat/test.poset-transformations.R
OncoSimulR/tests/testthat/test.sample-prob.R
OncoSimulR/tests/testthat/test.samplePop.R
OncoSimulR/tests/testthat/test.simuls-run-examples.R
OncoSimulR/tests/testthat/test.warning-mutPropGrowth.R
OncoSimulR/tests/testthat/test.wide2long.R
OncoSimulR/vignettes
OncoSimulR/vignettes/OncoSimulR.Rmd
OncoSimulR/vignettes/OncoSimulR.bib
OncoSimulR/vignettes/custom4.css
OncoSimulR/vignettes/gitHeadInfo.gin
OncoSimulR/vignettes/gitinfo.sty
OncoSimulR/vignettes/gitsetinfo.sty

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