TRONCO: TRONCO, an R package for TRanslational ONCOlogy

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The TRONCO (TRanslational ONCOlogy) R package collects algorithms to infer progression models via the approach of Suppes-Bayes Causal Network, both from an ensemble of tumors (cross-sectional samples) and within an individual patient (multi-region or single-cell samples). The package provides parallel implementation of algorithms that process binary matrices where each row represents a tumor sample and each column a single-nucleotide or a structural variant driving the progression; a 0/1 value models the absence/presence of that alteration in the sample. The tool can import data from plain, MAF or GISTIC format files, and can fetch it from the cBioPortal for cancer genomics. Functions for data manipulation and visualization are provided, as well as functions to import/export such data to other bioinformatics tools for, e.g, clustering or detection of mutually exclusive alterations. Inferred models can be visualized and tested for their confidence via bootstrap and cross-validation. TRONCO is used for the implementation of the Pipeline for Cancer Inference.

Author
Marco Antoniotti [ctb], Giulio Caravagna [aut, cre], Luca De Sano [aut], Alex Graudenzi [aut], Giancarlo Mauri [ctb], Bud Mishra [ctb], Daniele Ramazzotti [aut]
Date of publication
None
Maintainer
BIMIB Group <tronco@disco.unimib.it>
License
file LICENSE
Version
2.6.1
URLs

View on Bioconductor

Man pages

aCML
Atypical chronic myeloid leukemia dataset
AND
AND
annotate.description
annotate.description
annotate.stages
annotate.stages
as.adj.matrix
as.adj.matrix
as.alterations
as.alterations
as.bootstrap.scores
as.bootstrap.scores
as.colors
as.colors
as.conditional.probs
as.conditional.probs
as.confidence
as.confidence
as.description
as.description
as.events
as.events
as.events.in.patterns
as.events.in.patterns
as.events.in.sample
as.events.in.sample
as.gene
as.gene
as.genes
as.genes
as.genes.in.patterns
as.genes.in.patterns
as.genotypes
as.genotypes
as.hypotheses
as.hypotheses
as.joint.probs
as.joint.probs
as.kfold.eloss
as.kfold.eloss
as.kfold.posterr
as.kfold.posterr
as.kfold.prederr
as.kfold.prederr
as.marginal.probs
as.marginal.probs
as.models
as.models
as.parameters
as.parameters
as.pathway
as.pathway
as.patterns
as.patterns
as.samples
as.samples
as.selective.advantage.relations
as.selective.advantage.relations
as.stages
as.stages
as.types
as.types
as.types.in.patterns
as.types.in.patterns
cbio.query
cbio.query
change.color
change.color
consolidate.data
consolidate.data
crc_gistic
GISTIC example data
crc_maf
MAF example data
crc_plain
Plain mutation dataset
delete.event
delete.event
delete.gene
delete.gene
delete.hypothesis
delete.hypothesis
delete.model
delete.model
delete.pattern
delete.pattern
delete.samples
delete.samples
delete.type
delete.type
duplicates
duplicates
ebind
ebind
enforce.numeric
enforce.numeric
enforce.string
enforce.string
events.selection
events.selection
export.graphml
export.graphml
export.mutex
export,mutex
export.nbs.input
export.nbs.input
extract.MAF.HuGO.Entrez.map
extract.MAF.HuGO.Entrez.map
genes.table.report
genes.table.report
has.duplicates
has.duplicates
has.model
has.model
has.stages
has stages
hypothesis.add
hypothesis add
hypothesis.add.group
hypothesis add group
hypothesis.add.homologous
hypothesis.add.homologous
import.genotypes
import.genotypes
import.GISTIC
import.GISTIC
import.MAF
import.MAF
import.mutex.groups
import.mutex.groups
intersect.datasets
intersect.datasets
is.compliant
is.compliant
join.events
join.events
join.types
join.types
keysToNames
keysToNames
maf
MAF example data
muts
Simple mutation dataset
nameToKey
nameToKey
nevents
nevents
ngenes
ngenes
nhypotheses
Return the number of hypotheses in the dataset
npatterns
Return the number of patterns in the dataset
nsamples
nsamples
ntypes
ntypes
oncoprint
oncoprint
oncoprint.cbio
oncoprint.cbio
OR
OR
order.frequency
order.frequency
pathway.visualization
pathway.visualization
pheatmap
A function to draw clustered heatmaps.
rank.recurrents
rank.recurrents
rename.gene
rename.gene
rename.type
rename.type
samples.selection
samples.selection
sbind
sbind
ssplit
ssplit
stage
Stage information for test_dataset
TCGA.map.clinical.data
TCGA.map.clinical.data
TCGA.multiple.samples
TCGA.multiple.samples
TCGA.remove.multiple.samples
TCGA.remove.multiple.samples
TCGA.shorten.barcodes
TCGA.shorten.barcodes
test_dataset
A complete dataset with hypotheses
test_dataset_no_hypos
A complete dataset
test_model
A complete dataset with a reconstructed model
test_model_kfold
A complete dataset with a reconstructed model and...
trim
trim
tronco.bootstrap
tronco bootstrap
tronco.caprese
tronco caprese
tronco.capri
tronco capri
tronco.chowliu
Tronco Chow Liu
tronco.edmonds
Tronco Edmonds
tronco.gabow
Tronco Gabow
tronco.kfold.eloss
tronco.kfold.eloss
tronco.kfold.posterr
tronco.kfold.posterr. For details and examples regarding the...
tronco.kfold.prederr
tronco.kfold.prederr
tronco.pattern.plot
tronco.pattern.plot
tronco.plot
tronco.plot
tronco.prim
Tronco Prim
view
view
which.samples
which.samples
XOR
XOR

Files in this package

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