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

Peer review:

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

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:

evolutionphylogeneticssingle-cell

3.95 score 6 stars 1 packages 2 scripts 273 downloads 9 exports 62 dependencies

Last updated 1 years agofrom:42b4ac5649. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 11 2024
R-4.5-win-x86_64NOTENov 11 2024
R-4.5-linux-x86_64NOTENov 11 2024
R-4.4-win-x86_64NOTENov 11 2024
R-4.4-mac-x86_64NOTENov 11 2024
R-4.4-mac-aarch64NOTENov 11 2024
R-4.3-win-x86_64NOTENov 11 2024
R-4.3-mac-x86_64NOTENov 11 2024
R-4.3-mac-aarch64NOTENov 11 2024

Exports:annotate_treeget_mut_graphladderizemut_to_treeperform_nniplot_phylo_heatmaprun_scistreescore_treeto_phylo

Dependencies:apeaplotclicolorspacecpp11digestdplyrfansifarverfastmatchfsgenericsggfunggplot2ggplotifyggtreegluegridGraphicsgtableigraphisobandjsonlitelabelinglatticelazyevallifecyclemagrittrMASSMatrixmgcvmunsellnlmeparallelDistpatchworkphangornpillarpkgconfigplyrpurrrquadprogR6RColorBrewerRcppRcppArmadilloRcppParallelreshape2RhpcBLASctlrlangscalesstringistringrtibbletidygraphtidyrtidyselecttidytreetreeioutf8vctrsviridisLitewithryulab.utils