Man pages for Fraternalilab/BrepPhylo
BrepPhylo: R package for phylogenetic analysis of B cell repertoire
| addCloneToCompleted | Function to add a clone ID and its size to a file. |
| alignmentValidCodons | Function to ensure, that a given sequence alignment has valid... |
| cloneArborescence | Function to calculate the arborescence for a fully connected... |
| cloneLineage | Function to analyse B cell clone lineages, by producing an... |
| convertDNAStringSetToList | Function to parse DNAStringSet into nested list |
| curDateTime | Function to print the current date and the time. |
| doBatchCloneAnalysis | Perform phylogenetic inference & tree analysis in a batch |
| GermlineLikeness | Function to calculate germline likeness of a pre-selected... |
| getArborescence | Function to transform a distance matrix of observations into... |
| getColourVectorFromLevels | Function to generate a vector of colours from a vector of... |
| getCSEvents | Function to parse class-switching events from arborescence... |
| getDistancesFromTree | Function to calculate the distances for a B cell clone... |
| getDistPercentile | Function to calculate percentile of distance-from-germline... |
| getGermlineDistance | Function to calculate distance from germline for all... |
| getGermlineLikeness | Function to summarise Germline Likeness for repertoires |
| getSummaryFromBatch | Function to summarise distance-from-germline and CSR events... |
| IgPhyML | Function that calls IgPhyML to calculate a phylogenetic tree... |
| is.valid.IsotypeSwitch | Function that checks, whether a phylogenetic relationship in... |
| makeAlignmentPDF | Function to generate PDF files holding an alignment using the... |
| msaPrettyPrint_extended | Function extending the original "msa::msaPrettyPrint"... |
| plotCSRsummary | Function to plot class-switch recombination summaries of... |
| summariseCSR | Function to summarise details of different class-switch... |
| summariseGermlineDistance | Function to summarise distance-from-germline by clones |
| Vgermline | Collection of germline V DNA sequences |
| Vgermline_gapped | Collection of IMGT-gapped germline V DNA sequences |
