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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).

Version: 1.2.0
Depends: R (≥ 4.1.0)
Imports: ape, dplyr, ggplot2, ggtree, igraph, parallelDist, patchwork, phangorn, Rcpp, reshape2, RcppParallel, RhpcBLASctl, stringr, tidygraph
LinkingTo: Rcpp, RcppArmadillo, RcppParallel
Suggests: testthat (≥ 3.0.0)
Published: 2023-06-15
DOI: 10.32614/CRAN.package.scistreer
Author: Teng Gao [cre, aut], Evan Biederstedt [aut], Peter Kharchenko [aut], Yufeng Wu [aut]
Maintainer: Teng Gao <tgaoteng at gmail.com>
License: GPL-3
URL: https://github.com/kharchenkolab/scistreer, https://kharchenkolab.github.io/scistreer/
NeedsCompilation: yes
SystemRequirements: GNU make
Materials: README
CRAN checks: scistreer results

Documentation:

Reference manual: scistreer.pdf

Downloads:

Package source: scistreer_1.2.0.tar.gz
Windows binaries: r-devel: scistreer_1.2.0.zip, r-release: scistreer_1.2.0.zip, r-oldrel: scistreer_1.2.0.zip
macOS binaries: r-release (arm64): scistreer_1.2.0.tgz, r-oldrel (arm64): scistreer_1.2.0.tgz, r-release (x86_64): scistreer_1.2.0.tgz, r-oldrel (x86_64): scistreer_1.2.0.tgz
Old sources: scistreer archive

Reverse dependencies:

Reverse imports: numbat

Linking:

Please use the canonical form https://CRAN.R-project.org/package=scistreer to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.