Files in OncoSimulR

Forward Genetic Simulation of Cancer Progression with Epistasis

NAMESPACE

DESCRIPTION

build/vignette.rds

src/new_restrict.cpp

src/BNB_nr.cpp

src/Makevars.win

src/new_restrict.h

src/RcppExports.cpp

src/common_classes.h

src/debug_common.h

src/bnb_common.h

src/OncoSimulR_init.c

src/Makevars

src/install.libs.R

src/bnb_common.cpp

src/accessible_genotypes.cpp

src/BNB_v1.cpp

src/FitnessLandscape/chain.c

src/FitnessLandscape/drawings.h

src/FitnessLandscape/main_fl_statistics.c

src/FitnessLandscape/sort.c

src/FitnessLandscape/epistasis_type.c

src/FitnessLandscape/input.c

src/FitnessLandscape/LinearAlgebra.c

src/FitnessLandscape/gamma.c

src/FitnessLandscape/main_draw.c

src/FitnessLandscape/summary_statistics.h

src/FitnessLandscape/genotypes.h

src/FitnessLandscape/landscape.h

src/FitnessLandscape/main_webdraw.c

src/FitnessLandscape/genotypes.c

src/FitnessLandscape/main_generalizedchains_test.c

src/FitnessLandscape/common_drawings.c

src/FitnessLandscape/calculus.c

src/FitnessLandscape/random.h

src/FitnessLandscape/draw_land.c

src/FitnessLandscape/decomposition.c

src/FitnessLandscape/LinearAlgebra.h

src/FitnessLandscape/test_gamma.c

src/FitnessLandscape/generalized_chain.c

src/FitnessLandscape/main_fl_generate.c

src/FitnessLandscape/ordered_pairs.c

src/FitnessLandscape/random.c

src/FitnessLandscape/main_webmodels.c

src/FitnessLandscape/summary_statistics.c

src/FitnessLandscape/vector.c

src/FitnessLandscape/models.c

src/FitnessLandscape/landscape.c

src/FitnessLandscape/Makefile

src/FitnessLandscape/verbose.c

src/FitnessLandscape/verbose.h

src/FitnessLandscape/vector.h

src/FitnessLandscape/calculus.h

src/FitnessLandscape/models.h

src/FitnessLandscape/web/Magellan.model.mac.html

src/FitnessLandscape/web/Magellan.help.mac.html

src/FitnessLandscape/web/Magellan.known.mac.html

src/FitnessLandscape/web/help.png

src/FitnessLandscape/web/draw_custom.c

src/FitnessLandscape/web/landok.css

src/FitnessLandscape/web/Magellan.help.html

src/FitnessLandscape/web/Magellan.known.html

src/FitnessLandscape/web/HTML5_Logo_512.png

src/FitnessLandscape/web/web_common.c

src/FitnessLandscape/web/imgmagell.png

src/FitnessLandscape/web/server.h

src/FitnessLandscape/web/stat.png

src/FitnessLandscape/web/Magellan.main.html

src/FitnessLandscape/web/Magellan.custom.html

src/FitnessLandscape/web/land_js.js

src/FitnessLandscape/web/magellan.css

src/FitnessLandscape/web/Magellan.main.mac.html

src/FitnessLandscape/web/landmodel_js.js

src/FitnessLandscape/web/Magellan.model.html

src/FitnessLandscape/web/land.css

src/FitnessLandscape/web/webparam.h

src/FitnessLandscape/web/Magellan.custom.mac.html

src/FitnessLandscape/web/web_common.h

data/benchmark_3.RData

data/ex_missing_drivers_b11.RData

data/ex_missing_drivers_b12.RData

data/benchmark_1.RData

data/examplePosets.RData

data/examplesFitnessEffects.RData

data/mcfLs.RData

data/benchmark_1_0.05.RData

data/benchmark_2.RData

R/new-restrict.R R/OncoSimulR.R R/mutator.R R/rfitness.R R/fitness_landscape_utils.R R/RcppExports.R R/LOD_POM.R R/conversion-helpers.R R/from_genotype_utils.R R/generate-random-trees.R R/stacked-plots.R R/nem_transitive_reduction.R

vignettes/custom4.css

vignettes/relfunct.tex

vignettes/gitinfo.sty

vignettes/preamble.tex

vignettes/OncoSimulR.bib

vignettes/OncoSimulR.Rmd

vignettes/gitHeadInfo.gin

vignettes/gitsetinfo.sty

vignettes/relfunct.png

man/evalAllGenotypes.Rd man/plotClonePhylog.Rd man/to_Magellan.Rd man/plotFitnessLandscape.Rd man/plot.fitnessEffects.Rd man/benchmarks.Rd man/POM.Rd man/samplePop.Rd man/rfitness.Rd man/simOGraph.Rd man/examplePosets.Rd man/poset.Rd man/plotPoset.Rd man/mcfLs.Rd man/allFitnessEffects.Rd man/plot.oncosimul.Rd man/OncoSimulWide2Long.Rd man/examplesFitnessEffects.Rd man/oncoSimulIndiv.Rd man/example-missing-drivers.Rd tests/testthat.R

tests/README_names.txt

tests/manual/test.oncoSimulSample-limits-long.R tests/manual/test.mutator-long.R tests/manual/test.simuls-run-examples-long.R tests/manual/test.Z-warning-mutPropGrowth-long.R tests/manual/test.exercise-plotting-code-long.R tests/manual/test.driverCounts-long.R tests/manual/test.fixation-long.R tests/manual/test.Z-driverCounts-long.R tests/manual/test.mutator-oncoSimulSample-long.R tests/manual/test.warning-mutPropGrowth-long.R

tests/manual/README.txt

tests/manual/test.poset-transformations-long.R tests/manual/test.mutPropGrowth-long.R tests/manual/test.sample-prob-long.R tests/manual/test.per-gene-mutation-rates-long.R tests/manual/test.fitness-preds-long.R tests/manual/test.Z-sample-only-last-long.R tests/testthat/test.Z-fixation.R tests/testthat/test.driverCounts.R tests/testthat/test.Z-driverCounts.R tests/testthat/test.LOD_POM.R tests/testthat/test.oncoSimulSample-limits.R tests/testthat/test.samplePop.R tests/testthat/test.simuls-run-examples.R tests/testthat/test.exercise-rfitness.R tests/testthat/test.init-mutant.R tests/testthat/test.Z-oncoSimulIndiv.R tests/testthat/test.genot_fitness_to_epistasis.R tests/testthat/test.modules-root-no-root.R tests/testthat/test.magellan.R tests/testthat/test.exercise-to-Magellan.R tests/testthat/test.oncoSimulSample-failures.R tests/testthat/test.genotFitness.R tests/testthat/test.fixation.R tests/testthat/test.wide2long.R tests/testthat/test.per-gene-mutation-rates.R tests/testthat/test.oncoSimulIndiv-miscell.R tests/testthat/test.plotFitnessLandscape.R tests/testthat/test.Z-rfitness-landscape.R tests/testthat/test.Z-total-present-drivers.R tests/testthat/test.poset-transformations.R tests/testthat/test.sample-prob.R tests/testthat/test.fitness-preds.R tests/testthat/test.Z-mutator.R tests/testthat/test.flfast-mutator.R tests/testthat/test.warning-mutPropGrowth.R tests/testthat/test.exercise-plotting-code.R tests/testthat/test.mutator-oncoSimulSample.R tests/testthat/test.flfast-additional.R tests/testthat/test.all-fitness.R tests/testthat/test.Z-magellan.R tests/testthat/test.accessible_genotypes.R tests/testthat/test.epist-order-modules.R tests/testthat/test.mutator.R tests/testthat/test.Z-sample-only-last.R tests/testthat/test.mutPropGrowth.R tests/testthat/test.Z-all-fitness.R

inst/testdata_fee.RData

inst/NEWS

inst/CITATION

inst/doc/OncoSimulR.R

inst/doc/OncoSimulR.html

inst/doc/OncoSimulR.Rmd inst/miscell/benchmark_3.R inst/miscell/benchmark_1.R inst/miscell/large_pop_size.R inst/miscell/benchmark_2.R inst/miscell/benchmark_1_0.05.R inst/miscell/large_num_genes.R inst/miscell/large_num_genes_0.05.R

inst/miscell/example-binom-problems.cpp

OncoSimulR documentation built on Nov. 8, 2020, 8:31 p.m.