# CBN2Path: an R/Bioconductor package for the analysis of cancer progression pathways using Conjunctive Bayesian Networks

## Documentation for package ‘CBN2Path’ version 1.2.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

base2Indexing | base2Indexing
base2IndVec | base2IndVec
bcbn | B-CBN
ctcbn | CT-CBN
ctcbnSingle | CT-CBN Single Batch
edgeMarginalized | edgeMarginalized
generateData | Generate Data
generateMatrixGenotypes | generateMatrixGenotypes
generateTCGAMatrix | Generate TCGA Genotype Matrix
genotypeFeasibility | genotypeFeasibility
genotypeMatrixMutator | genotypeMatrixMutator
getExamples | Get paths to examples
getRawTCGAData | Get Raw TCGA Data
hcbn | H-CBN
hcbnSingle | H-CBN Single Batch
jensenShannonDivergence | jensenShannonDivergence
pathEdgeMapper | pathEdgeMapper
pathNormalization | pathNormalization
pathProbCBN | pathProbCBN: quantifies pathway probabilities using the output of CT-CBN or H-CBN
pathProbQuartetBCBN | pathProbQuartetBCBN
pathProbQuartetCTCBN | pathProbQuartetCTCBN
pathProbQuartetHCBN | pathProbQuartetHCBN
pathProbQuartetRCBN | pathProbQuartetRCBN
pathProbSSWM | pathProbSSWM
pathwayCompatibilityQuartet | pathwayCompatibilityQuartet
pathwayFeasibility | pathwayFeasibility
pathwayGenotypeCompatibility | pathwayGenotypeCompatibility
pathwayWeightingRCBN | pathwayWeightingRCBN
permutations | permutations
posetWeightingRCBN | posetWeightingRCBN
predictability | predictability
readLambda | Read a .lambda file
readPattern | Read a .pat file
readPoset | Read a .poset file
readTime | Read a .time file
Spock | Poset and pattern/lambda data
transitiveClosure | Transitive Closure
visualizeCBNModel | Visualize CBN Model
visualizeFitnessLandscape | Visualize Fitness Landscape
visualizeProbabilities | Visualize Pathway Probabilities