Man pages for benstory/mitoClone2
Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations
| bam2R_10x | Read nucleotide counts from a 10x Genomics .bam file |
| baseCountsFromBamList | Create a list object from a list of single-cell BAM files... |
| clusterMetaclones | Cluster mutations into clones - following the tree structure |
| data | Mitochondrial exclusionlist |
| getAlleleCount | mutationCalls counts accessor |
| getCloneLikelihood | mutationCalls accessors |
| getVarsCandidate | mutationCalls cluster accessor |
| mitoPlot | Plot clone-specific variants in circular plots |
| mut2GR | Convert mutation string to GRanges |
| mutationCalls-class | mutationCalls class |
| mutationCallsFromCohort | Create a mutationCalls objects from nucleotide base calls and... |
| mutationCallsFromExclusionlist | Create a mutationCalls object from nucleotide base calls... |
| mutationCallsFromMatrix | mutationCalls constructor |
| overwriteMetaclones | Manually overwrite clustering of mutations into clones |
| plotClones | Plot clonal assignment of single cells |
| pullcountsVars | Pull variant counts |
| quick_cluster | Quick clustering of mutations |
| removeWindow | Remove mutations that occuring at the same site |
| setVarsCandidate | mutationCalls cluster setter |
| varCluster | Inference of mutational trees by of single cell mutational... |
