API for broadinstitute/ichorCNA
A tool for estimating the fraction of tumor in ultra-low-pass whole genome sequencing (ULP-WGS) of cell-free DNA
| Global functions | |
|---|---|
| HMMsegment | Source code |
| betapdflog | Source code |
| completeLikelihoodFun | Source code |
| computeBIC | Source code |
| correctIntegerCN | Source code |
| correctReadCounts | Source code |
| dirichletpdf | Source code |
| dirichletpdflog | Source code |
| estimateMixWeightsParamMap | Source code |
| estimateParamsMap | Source code |
| estimatePrecisionParamMap | Source code |
| excludeCentromere | Source code |
| filterByMappabilityScore | Source code |
| filterByTargetedSequences | Source code |
| filterEmptyChr | Source code |
| gammapdflog | Source code |
| get2ComponentMixture | Source code |
| get2and3ComponentMixture | Source code |
| getDefaultParameters | Source code |
| getGender | Source code |
| getGenomeWidePositions | Source code |
| getSeqInfo | Source code |
| getTransitionMatrix | Source code |
| ichorCNA | Man page |
| ichorCNA-package | Man page |
| keepChr | Source code |
| loadReadCountsFromWig | Source code |
| logRbasedCN | Source code |
| normalize | Source code |
| normalizeByPanelOrMatchedNormal | Source code |
| outputHMM | Source code |
| outputParametersToFile | Source code |
| plotCNlogRByChr | Source code |
| plotChrLines | Source code |
| plotCorrectionGenomeWide | Source code |
| plotGWSolution | Source code |
| plotParam | Source code |
| plotSolutions | Source code |
| priorProbs | Source code |
| runEM | Source code |
| runViterbi | Source code |
| segmentData | Source code |
| selectFemaleChrXSolution | Source code |
| setGenomeStyle | Source code |
| stLikelihood | Source code |
| tdistPDF | Source code |
| wigToGRanges | Source code |
