API for JEFworks/HoneyBADGER
HMM-integrated Bayesian approach for detecting CNV and LOH events using single-cell RNA-seq data
| Global functions | |
|---|---|
| .ChIPseekerEnv | Source code |
| HoneyBADGER | Man page |
| HoneyBADGER-class | Man page |
| HoneyBADGER_calcAlleleCnvBoundaries | Man page |
| HoneyBADGER_calcAlleleCnvProb | Man page |
| HoneyBADGER_calcCombCnvProb | Man page |
| HoneyBADGER_calcGexpCnvBoundaries | Man page |
| HoneyBADGER_calcGexpCnvProb | Man page |
| HoneyBADGER_plotAlleleProfile | Man page |
| HoneyBADGER_plotGexpProfile | Man page |
| HoneyBADGER_plotSmoothedAlleleProfile | Man page |
| HoneyBADGER_retestIdentifiedCnvs | Man page |
| HoneyBADGER_setAlleleMats | Man page |
| HoneyBADGER_setGeneFactors | Man page |
| HoneyBADGER_setGexpDev | Man page |
| HoneyBADGER_setGexpMats | Man page |
| HoneyBADGER_setMvFit | Man page |
| HoneyBADGER_summarizeResults | Man page |
| HoneyBADGER_visualizeResults | Man page |
| TXID2EG | Source code |
| TXID2EGID | Source code |
| TXID2TXEG | Source code |
| annotatePeak | Source code |
| as.GRanges | Source code |
| as.data.frame.csAnno | Source code |
| calcAlleleCnvBoundaries | Man page Source code |
| calcAlleleCnvProb | Man page Source code |
| calcCombCnvProb | Man page Source code |
| calcGexpCnvBoundaries | Man page Source code |
| calcGexpCnvProb | Man page Source code |
| cov.sc | Man page |
| getAlleleCount | Man page |
| getAnnoStat | Source code |
| getCellAlleleCount | Man page |
| getCoverage | Man page |
| getFirstHitIndex | Source code |
| getGene | Source code |
| getGenomicAnnoStat | Source code |
| getGenomicAnnotation | Source code |
| getGenomicAnnotation.internal | Source code |
| getHetRate | Man page |
| getNearestFeatureIndicesAndDistances | Source code |
| getSnpMats | Man page Source code |
| getSnpMats10X | Man page |
| get_exonList | Source code |
| get_intronList | Source code |
| gexp | Man page |
| isHet | Man page |
| isHetAlt | Man page |
| isPeakFeatureOverlap | Source code |
| loadTxDb | Source code |
| plotAlleleProfile | Man page Source code |
| plotGexpProfile | Man page Source code |
| r | Man page |
| ref | Man page |
| setAlleleMats | Man page Source code |
| setGeneFactors | Man page Source code |
| setGexpDev | Man page Source code |
| setGexpMats | Man page Source code |
| setMvFit | Man page Source code |
| summarizeMatrix | Source code |
| trimSnps | Man page |
| updateGenomicAnnotation | Source code |
