TRONCO: TRONCO, an R package for TRanslational ONCOlogy

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.

AuthorMarco Antoniotti [ctb], Giulio Caravagna [aut, cre], Luca De Sano [aut], Alex Graudenzi [aut], Giancarlo Mauri [ctb], Bud Mishra [ctb], Daniele Ramazzotti [aut]
Date of publicationNone
MaintainerBIMIB Group <tronco@disco.unimib.it>
Licensefile LICENSE
Version2.6.1
https://sites.google.com/site/troncopackage/

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

Functions

aCML Man page
AND Man page
annotate.description Man page
annotate.stages Man page
as.adj.matrix Man page
as.alterations Man page
as.bootstrap.scores Man page
as.colors Man page
as.conditional.probs Man page
as.confidence Man page
as.description Man page
as.events Man page
as.events.in.patterns Man page
as.events.in.sample Man page
as.gene Man page
as.genes Man page
as.genes.in.patterns Man page
as.genotypes Man page
as.hypotheses Man page
as.joint.probs Man page
as.kfold.eloss Man page
as.kfold.posterr Man page
as.kfold.prederr Man page
as.marginal.probs Man page
as.models Man page
as.parameters Man page
as.pathway Man page
as.patterns Man page
as.samples Man page
as.selective.advantage.relations Man page
as.stages Man page
as.types Man page
as.types.in.patterns Man page
cbio.query Man page
change.color Man page
consolidate.data Man page
crc_gistic Man page
crc_maf Man page
crc_plain Man page
delete.event Man page
delete.gene Man page
delete.hypothesis Man page
delete.model Man page
delete.pattern Man page
delete.samples Man page
delete.type Man page
duplicates Man page
ebind Man page
enforce.numeric Man page
enforce.string Man page
events.selection Man page
export.graphml Man page
export.mutex Man page
export.nbs.input Man page
extract.MAF.HuGO.Entrez.map Man page
genes.table.report Man page
has.duplicates Man page
has.model Man page
has.stages Man page
hypothesis.add Man page
hypothesis.add.group Man page
hypothesis.add.homologous Man page
import.genotypes Man page
import.GISTIC Man page
import.MAF Man page
import.mutex.groups Man page
intersect.datasets Man page
is.compliant Man page
join.events Man page
join.types Man page
keysToNames Man page
maf Man page
muts Man page
nameToKey Man page
nevents Man page
ngenes Man page
nhypotheses Man page
npatterns Man page
nsamples Man page
ntypes Man page
oncoprint Man page
oncoprint.cbio Man page
OR Man page
order.frequency Man page
pathway.visualization Man page
pheatmap Man page
rank.recurrents Man page
rename.gene Man page
rename.type Man page
samples.selection Man page
sbind Man page
ssplit Man page
stage Man page
TCGA.map.clinical.data Man page
TCGA.multiple.samples Man page
TCGA.remove.multiple.samples Man page
TCGA.shorten.barcodes Man page
test_dataset Man page
test_dataset_no_hypos Man page
test_model Man page
test_model_kfold Man page
trim Man page
tronco.bootstrap Man page
tronco.caprese Man page
tronco.capri Man page
tronco.chowliu Man page
tronco.edmonds Man page
tronco.gabow Man page
tronco.kfold.eloss Man page
tronco.kfold.posterr Man page
tronco.kfold.prederr Man page
tronco.pattern.plot Man page
tronco.plot Man page
tronco.prim Man page
view Man page
which.samples Man page
XOR Man page

Files

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

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