Files in BIMIB-DISCo/TRONCO
TRONCO, an R package for TRanslational ONCOlogy
.Rbuildignore
.github/.gitignore
.github/workflows/check-bioc.yml
.gitignore
DESCRIPTION
LICENSE.md
NAMESPACE
R/as.functions.R
R/bootstrap.R
R/caprese.algorithm.R
R/capri.algorithm.R
R/capri.hypotheses.R
R/chow.liu.algorithm.R
R/correctness.R
R/create.model.R
R/data.R
R/editing.functions.R
R/edmonds.algorithm.R
R/external.R
R/gabow.algorithm.R
R/loading.R
R/lregfit.R
R/prim.algorithm.R
R/selection.R
R/statistics.R
R/tronco.R
R/visualization.R
R/which.functions.R
R/zzz.R
README.md
_pkgdown.yml
data/aCML.RData
data/crc_gistic.RData
data/crc_maf.RData
data/crc_plain.RData
data/maf.csv
data/muts.RData
data/stage.RData
data/test_dataset.RData
data/test_dataset_no_hypos.RData
data/test_model.RData
data/test_model_kfold.RData
inst/NEWS.Rd
man/AND.Rd
man/OR.Rd
man/TCGA.map.clinical.data.Rd
man/TCGA.multiple.samples.Rd
man/TCGA.remove.multiple.samples.Rd
man/TCGA.shorten.barcodes.Rd
man/XOR.Rd
man/aCML.Rd
man/annotate.description.Rd
man/annotate.stages.Rd
man/as.adj.matrix.Rd
man/as.alterations.Rd
man/as.bootstrap.scores.Rd
man/as.colors.Rd
man/as.conditional.probs.Rd
man/as.confidence.Rd
man/as.description.Rd
man/as.events.Rd
man/as.events.in.patterns.Rd
man/as.events.in.sample.Rd
man/as.gene.Rd
man/as.genes.Rd
man/as.genes.in.patterns.Rd
man/as.genotypes.Rd
man/as.hypotheses.Rd
man/as.joint.probs.Rd
man/as.kfold.eloss.Rd
man/as.kfold.posterr.Rd
man/as.kfold.prederr.Rd
man/as.marginal.probs.Rd
man/as.models.Rd
man/as.parameters.Rd
man/as.pathway.Rd
man/as.patterns.Rd
man/as.samples.Rd
man/as.selective.advantage.relations.Rd
man/as.stages.Rd
man/as.types.Rd
man/as.types.in.patterns.Rd
man/change.color.Rd
man/consolidate.data.Rd
man/crc_gistic.Rd
man/crc_maf.Rd
man/crc_plain.Rd
man/delete.event.Rd
man/delete.gene.Rd
man/delete.hypothesis.Rd
man/delete.model.Rd
man/delete.pattern.Rd
man/delete.samples.Rd
man/delete.type.Rd
man/duplicates.Rd
man/ebind.Rd
man/enforce.numeric.Rd
man/enforce.string.Rd
man/events.selection.Rd
man/export.graphml.Rd
man/export.mutex.Rd
man/export.nbs.input.Rd
man/extract.MAF.HuGO.Entrez.map.Rd
man/genes.table.report.Rd
man/has.duplicates.Rd
man/has.model.Rd
man/has.stages.Rd
man/hypothesis.add.Rd
man/hypothesis.add.group.Rd
man/hypothesis.add.homologous.Rd
man/import.GISTIC.Rd
man/import.MAF.Rd
man/import.genotypes.Rd
man/import.model.Rd
man/import.mutex.groups.Rd
man/intersect.datasets.Rd
man/is.compliant.Rd
man/join.events.Rd
man/join.types.Rd
man/keysToNames.Rd
man/maf.Rd
man/muts.Rd
man/nameToKey.Rd
man/nevents.Rd
man/ngenes.Rd
man/nhypotheses.Rd
man/npatterns.Rd
man/nsamples.Rd
man/ntypes.Rd
man/oncoprint.Rd
man/oncoprint.cbio.Rd
man/order.frequency.Rd
man/pathway.visualization.Rd
man/pheatmap.Rd
man/rank.recurrents.Rd
man/rename.gene.Rd
man/rename.type.Rd
man/samples.selection.Rd
man/sbind.Rd
man/ssplit.Rd
man/stage.Rd
man/test_dataset.Rd
man/test_dataset_no_hypos.Rd
man/test_model.Rd
man/test_model_kfold.Rd
man/trim.Rd
man/tronco.bootstrap.Rd
man/tronco.caprese.Rd
man/tronco.capri.Rd
man/tronco.chowliu.Rd
man/tronco.edmonds.Rd
man/tronco.gabow.Rd
man/tronco.kfold.eloss.Rd
man/tronco.kfold.posterr.Rd
man/tronco.kfold.prederr.Rd
man/tronco.pattern.plot.Rd
man/tronco.plot.Rd
man/tronco.prim.Rd
man/view.Rd
man/which.samples.Rd
tests/testthat.R
tests/testthat/test_as_function.R
tests/testthat/test_editing.R
tests/testthat/test_hypotheses.R
tests/testthat/test_statistics.R
tests/testthat/test_tronco.R
tests/testthat/test_visualization.R
vignettes/.gitignore
vignettes/f1_introduction.rmd
vignettes/f2_loading_data.Rmd
vignettes/f3_data_visualization.Rmd
vignettes/f4_data_manipulation.Rmd
vignettes/f5_model_inference.Rmd
vignettes/f6_post_reconstruction.Rmd
vignettes/f7_import_export.Rmd
