aCML	aCML
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	crc_gistic
crc_maf	crc_maf
crc_plain	crc_plain
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.model	import.model
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
muts	muts
nameToKey	nameToKey
nevents	nevents
ngenes	ngenes
nhypotheses	nhypotheses
npatterns	npatterns
nsamples	nsamples
ntypes	ntypes
oncoprint	oncoprint
oncoprint.cbio	oncoprint.cbio
OR	OR
order.frequency	order.frequency
pathway.visualization	pathway.visualization
pheatmap	pheatmap
rank.recurrents	rank.recurrents
rename.gene	rename.gene
rename.type	rename.type
samples.selection	samples.selection
sbind	sbind
ssplit	ssplit
stage	stage
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	test_dataset
test_dataset_no_hypos	test_dataset_no_hypos
test_model	test_model
test_model_kfold	test_model_kfold
trim	trim
tronco.bootstrap	tronco.bootstrap
tronco.caprese	tronco.caprese
tronco.capri	tronco.capri
tronco.chowliu	tronco.chowliu
tronco.edmonds	tronco.edmonds
tronco.gabow	tronco.gabow
tronco.kfold.eloss	tronco.kfold.eloss
tronco.kfold.posterr	tronco.kfold.posterr
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
