R Observatory: Metrics for scistreer version 1.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

scistreer

1.2.1Package record

Maximum-Likelihood Perfect Phylogeny Inference at Scale

1packages depend

5.5Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Teng GaoCRAN page ↗GitHub ↗Website ↗

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).

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("scistreer", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("kharchenkolab/scistreer")

Development version from kharchenkolab/scistreer. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-scistreer

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

2NOTE11OK

Check messages

NOTEdependencies in R coder-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Namespace in Imports field not imported from:
  ‘Rcpp’
All declared Imports should be used.

CRAN check page ↗

Slowest check: 4.6 min · r-devel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTE2026-08-05
ERROR10 OK, 2 NOTE, 1 ERROR2026-07-30
NOTE11 OK, 2 NOTE2026-06-09
ERROR10 OK, 2 NOTE, 1 ERROR2026-06-08
NOTE11 OK, 2 NOTE2026-05-10

Show 4 earlier changesHide 4 earlier changes

ERROR10 OK, 2 NOTE, 1 ERROR2026-05-03
NOTE9 OK, 5 NOTE2026-04-22
ERROR8 OK, 5 NOTE, 1 ERROR2026-04-18
NOTE9 OK, 5 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.1

READMEYes · 225 wordsVignettesNoNEWSNoCitation fileNoWebsiteYes · pkgdown

Help pages: 17 (2 internal)
Examples that run: 100%9 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 89%
Help pages citing references: 0%

How these are measured

Downloads

5.5K

CRAN downloads in the past year

Rank #5,932 · ~15/day · ~460/mo

Releases R versions

Daily download trend is not available in this view yet.

46030 days

1.4K90 days

5.5K1 year

Compare downloads with other packages →

Also on522 r2u1K bioconda

How downloads are counted

Repository

kharchenkolab/scistreer ↗Organization: kharchenkolab

9Stars

3Forks

0Open issues

0Open PRs

0Releases

117Commits

4Commit identities

evolutionphylogeneticssingle-cell

License file reads as GPL-3.0 · 117 commits · Last activity 2026-02-04 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 0
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2024-12-11 · 72026-09-15 · 9

How these are measured

PracticesBeta

5 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/kharchenkolab/scistreer on 2026-10-22.

Continuous integration (2)

GitHub ActionsCircleCI

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-02-04 · The repository has a site deploy workflow

pkgdown site last built 2023-01-05, before release 1.2.1 (2026-02-05)

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Installing scistreer adds 44 packages (29 with compiled code, 44 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, igraph 4.8 MB. 1 more not on CRAN is not measured.

Depends (1)

R >= 4.1.0

Imports (14)

ape dplyr ggplot2 ggtree igraph parallelDist patchwork phangorn Rcpp reshape2 RcppParallel RhpcBLASctl stringr tidygraph

LinkingTo (3)

Rcpp RcppArmadillo RcppParallel

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

numbat

How these are counted

Code & Tests

Datasets

People & History

People (4)

Teng Gao

Maintainer since 1.0.0 (2022), Author

Evan Biederstedt

Author

Peter Kharchenko

Author

Yufeng Wu

Author

Releases (5)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.2.1Latest
record
2026-02-05 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.2.0
record
2023-06-15 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.1.0
record
2023-01-06 · diff ↗ ·
added 1 export
ladderize
1.0.1
record
2022-11-25 · diff ↗ ·
added 3 exports
mut_to_tree, perform_nni, score_tree
1.0.0
record
2022-11-21
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-11-21
Total releases: 5 / 4 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1.0
Bundled data: 107 KB / 6 files
Download size: 123 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("scistreer")

Format

Gao, T., Biederstedt, E., Kharchenko, P., & Wu, Y. (2026). scistreer: Maximum-Likelihood Perfect Phylogeny Inference at Scale (Version 1.2.1) [Computer software]. https://doi.org/10.32614/CRAN.package.scistreer

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for scistreer version 1.2.1 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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