Package: scistreer 1.2.0

Teng Gao

scistreer: Maximum-Likelihood Perfect Phylogeny Inference at Scale

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).

Authors:Teng Gao [cre, aut], Evan Biederstedt [aut], Peter Kharchenko [aut], Yufeng Wu [aut]

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scistreer.pdf |scistreer.html✨
scistreer/json (API)

# Install 'scistreer' in R:

install.packages('scistreer', repos = c('https://kharchenkolab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/kharchenkolab/scistreer/issues

Pkgdown site:https://kharchenkolab.github.io

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

P_example - Example genotype probability matrix
P_small - Smaller example genotype probability matrix
gtree_small - Smaller example annotated tree built from P_small
mut_nodes_small - Mutation placements calculated from tree_small and P_small
tree_small - Smaller example tree built from P_small
tree_upgma - Example tree built using UPGMA from P_small

On CRAN:

evolution phylogenetics single-cell cpp

4.02 score 7 stars 1 packages 2 scripts 335 downloads 9 exports 62 dependencies

Last updated 2 years agofrom:42b4ac5649. Checks:1 OK, 10 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 09 2025
R-4.5-win-x86_64	NOTE	Feb 09 2025
R-4.5-mac-x86_64	NOTE	Feb 09 2025
R-4.5-mac-aarch64	NOTE	Feb 09 2025
R-4.5-linux-x86_64	NOTE	Feb 09 2025
R-4.4-win-x86_64	NOTE	Feb 09 2025
R-4.4-mac-x86_64	NOTE	Feb 09 2025
R-4.4-mac-aarch64	NOTE	Feb 09 2025
R-4.3-win-x86_64	NOTE	Feb 09 2025
R-4.3-mac-x86_64	NOTE	Feb 09 2025
R-4.3-mac-aarch64	NOTE	Feb 09 2025

Exports:annotate_tree get_mut_graph ladderize mut_to_tree perform_nni plot_phylo_heatmap run_scistree score_tree to_phylo

Dependencies:ape aplot cli colorspace cpp11 digest dplyr fansi farver fastmatch fs generics ggfun ggplot2 ggplotify ggtree glue gridGraphics gtable igraph isoband jsonlite labeling lattice lazyeval lifecycle magrittr MASS Matrix mgcv munsell nlme parallelDist patchwork phangorn pillar pkgconfig plyr purrr quadprog R6 RColorBrewer Rcpp RcppArmadillo RcppParallel reshape2 RhpcBLASctl rlang scales stringi stringr tibble tidygraph tidyr tidyselect tidytree treeio utf8 vctrs viridisLite withr yulab.utils

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Find maximum lilkelihood assignment of mutations on a tree	annotate_tree
Convert a single-cell phylogeny with mutation placements into a mutation graph	get_mut_graph
Smaller example annotated tree built from P_small	gtree_small
From ape; will remove once new ape version is released https://github.com/emmanuelparadis/ape/issues/54	ladderize
Mutation placements calculated from tree_small and P_small	mut_nodes_small
Transfer mutation assignment onto a single-cell phylogeny	mut_to_tree
Example genotype probability matrix	P_example
Smaller example genotype probability matrix	P_small
Maximum likelihood tree search via NNI	perform_nni
Plot phylogeny and mutation heatmap	plot_phylo_heatmap
Run the scistree workflow	run_scistree
Score a tree based on maximum likelihood	score_tree
Convert the phylogeny from tidygraph to phylo object modified from R package alakazam, converts a tbl_graph to a phylo object	to_phylo
Smaller example tree built from P_small	tree_small
Example tree built using UPGMA from P_small	tree_upgma