zhouzilu/DENDRO: Dna based EvolutioNary tree preDiction by scRna-seq technOlogy

We propose DENDRO, a statistical framework takes scRNA-seq data for a tumor and accurately reconstructs its phylogeny, assigning each single cell from the scRNA-seq data to a subclone. Our approach allows us to (1) cluster cells based on genomic profiles while accounting for transcriptional bursting, technical dropout and sequencing error, as benchmarked on in silico mixture and a spike-in analysis, (2) make robust mutation profile inference in subclonal resolution, and (3) perform DNA-RNA joint analysis with same set of cells and examine the relationship between transcriptomic variation and mutation profile. In addition,

install.packages("remotes")
remotes::install_github("zhouzilu/DENDRO")