API for navinlabcode/copykit
CopyKit
| Global functions | |
|---|---|
| %!in% | Man page |
| %>% | Man page |
| .CopyKit | Man page |
| .countBreakpoints | Man page Source code |
| .invft | Source code |
| .multipcf | Source code |
| .quiet | Source code |
| CopyKit | Man page Source code |
| CopyKit-class | Man page |
| CopyKit-internals | Man page |
| `%!in%` | Source code |
| bincounts | Man page |
| bincounts,CopyKit-method | Man page |
| calcConsensus | Man page Source code |
| calcInteger | Man page Source code |
| calcRatios | Man page Source code |
| combine.func | Man page |
| compactMulti | Source code |
| consensus | Man page |
| consensus,CopyKit-method | Man page |
| consensus<- | Man page |
| consensus<-,CopyKit-method | Man page |
| consensusPhylo | Man page |
| consensusPhylo,CopyKit-method | Man page |
| consensusPhylo<- | Man page |
| consensusPhylo<-,CopyKit-method | Man page |
| copykit_example | Man page Source code |
| copykit_example_filtered | Man page Source code |
| copykit_obj_filt_rle | Man page |
| copykit_obj_filt_umap | Man page |
| copykit_obj_rle | Man page |
| distMat | Man page |
| distMat,CopyKit-method | Man page |
| distMat<- | Man page |
| distMat<-,CopyKit-method | Man page |
| doMultiPCF | Source code |
| expandMulti | Source code |
| findAneuploidCells | Man page Source code |
| findClusters | Man page Source code |
| findMarksMulti | Source code |
| findOutliers | Man page Source code |
| findSuggestedK | Man page Source code |
| findVariableGenes | Man page Source code |
| find_scaffold_genes | Man page Source code |
| getArmandChromStop | Source code |
| getArms | Source code |
| getMad | Source code |
| graph | Man page |
| graph,CopyKit-method | Man page |
| graph<- | Man page |
| graph<-,CopyKit-method | Man page |
| hdbscanCBI | Man page Source code |
| hg19_genes | Man page |
| hg19_rg | Man page |
| hg38_genes | Man page |
| hg38_grangeslist | Man page |
| igraph-class | Man page |
| inferMrca | Man page Source code |
| knnSmooth | Man page Source code |
| l2e.normal.sd | Man page Source code |
| leidenCBI | Man page Source code |
| logNorm | Man page Source code |
| louvainCBI | Man page Source code |
| markMultiPotts | Source code |
| medianFilter | Source code |
| mergeLevels | Man page |
| mock_bincounts | Man page Source code |
| multiPCFcompact | Source code |
| numericArms | Source code |
| numericChrom | Source code |
| ocean.balance | Man page Source code |
| ocean_balance_hex | Man page |
| overdispersion | Man page Source code |
| parCor | Man page Source code |
| phylo | Man page |
| phylo,CopyKit-method | Man page |
| phylo<- | Man page |
| phylo<-,CopyKit-method | Man page |
| plotAlluvial | Man page Source code |
| plotConsensusLine | Man page Source code |
| plotFreq | Man page Source code |
| plotGeneCopy | Man page Source code |
| plotHeatmap | Man page Source code |
| plotMetrics | Man page Source code |
| plotPca | Man page Source code |
| plotPhylo | Man page Source code |
| plotRatio | Man page Source code |
| plotScree | Man page Source code |
| plotSuggestedK | Man page Source code |
| plotUmap | Man page Source code |
| plotVariableGenes | Man page Source code |
| pullOutContent | Source code |
| ratios | Man page |
| ratios,CopyKit-method | Man page |
| runConsensusPhylo | Man page Source code |
| runCountReads | Man page Source code |
| runDistMat | Man page Source code |
| runMetrics | Man page Source code |
| runMultiPcfSubset | Source code |
| runPca | Man page Source code |
| runPhylo | Man page Source code |
| runSegmentation | Man page Source code |
| runUmap | Man page Source code |
| runVarbin | Man page Source code |
| runVst | Man page Source code |
| sawMarkM | Source code |
| segment_ratios | Man page |
| segment_ratios,CopyKit-method | Man page |
| selectFastMultiPcf | Source code |
| show | Man page |
| show,CopyKit-method | Man page |
| subclones_pal | Man page Source code |
| superclones_pal | Man page Source code |
