R pipeline for computing persistent homology in topological data analysis. See https://doi.org/10.21105/joss.00860 for more details.

Simple R Codes For Visualizing Genomics Data

LineageHomology uses phylogenies with reconstructed ancestral states to define groups of phylogenetic tips that have gained their states through homologous inheritance or de novo acquisition. LineageHomology can be applied to pathogen phylogeography to define transmission lineages and singletons and derive simple estimates of importation and loc…