Package: scistreer 1.2.0
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:
scistreer_1.2.0.tar.gz
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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
- 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
evolutionphylogeneticssingle-cell
Last updated 1 years agofrom:42b4ac5649. Checks:OK: 1 NOTE: 8. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 11 2024 |
R-4.5-win-x86_64 | NOTE | Nov 11 2024 |
R-4.5-linux-x86_64 | NOTE | Nov 11 2024 |
R-4.4-win-x86_64 | NOTE | Nov 11 2024 |
R-4.4-mac-x86_64 | NOTE | Nov 11 2024 |
R-4.4-mac-aarch64 | NOTE | Nov 11 2024 |
R-4.3-win-x86_64 | NOTE | Nov 11 2024 |
R-4.3-mac-x86_64 | NOTE | Nov 11 2024 |
R-4.3-mac-aarch64 | NOTE | Nov 11 2024 |
Exports:annotate_treeget_mut_graphladderizemut_to_treeperform_nniplot_phylo_heatmaprun_scistreescore_treeto_phylo
Dependencies:apeaplotclicolorspacecpp11digestdplyrfansifarverfastmatchfsgenericsggfunggplot2ggplotifyggtreegluegridGraphicsgtableigraphisobandjsonlitelabelinglatticelazyevallifecyclemagrittrMASSMatrixmgcvmunsellnlmeparallelDistpatchworkphangornpillarpkgconfigplyrpurrrquadprogR6RColorBrewerRcppRcppArmadilloRcppParallelreshape2RhpcBLASctlrlangscalesstringistringrtibbletidygraphtidyrtidyselecttidytreetreeioutf8vctrsviridisLitewithryulab.utils