Maximum-Likelihood Perfect Phylogeny Inference at Scale
Find maximum lilkelihood assignment of mutations on a tree
Convert a single-cell phylogeny with mutation placements into a mutati...
Annotate the direct upstream or downstream mutations on the edges
From ape; will remove once new ape version is released https://github....
Transfer mutation assignment onto a single-cell phylogeny
Maximum likelihood tree search via NNI
Plot phylogeny and mutation heatmap
Run the scistree workflow
Score a tree based on maximum likelihood
Convert the phylogeny from tidygraph to phylo object modified from R p...
Annotate the direct upstream or downstream node on the edges
Fast maximum-likelihood phylogeny inference from noisy single-cell data using the 'ScisTree' algorithm by Yufeng Wu (2019) <doi:10.1093/bioinformatics/btz676>. 'scistreer' provides an 'R' interface and improves speed via 'Rcpp' and 'RcppParallel', making the method applicable to massive single-cell datasets (>10,000 cells).