R Observatory: Metrics for scPloidy version 0.6.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

scPloidy

0.6.2Package record

Infer Ploidy of Single Cells

0packages depend

6.6Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Fumihiko TakeuchiCRAN page ↗GitHub ↗Issues ↗

Compute ploidy of single cells (or nuclei) based on single-cell (or single-nucleus) ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) data https://github.com/fumi-github/scPloidy.

Install

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

install.packages("scPloidy", 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("fumi-github/scPloidy")

Development version from fumi-github/scPloidy. 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-scploidy

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

13OK

CRAN check page ↗

Slowest check: 9.5 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.6.2

READMEYes · 157 wordsVignettesYes · 2 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 6 (1 internal)
Examples that run: 50%1 run in a plain check · 1 never run
Exported functions with examples: 0%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 17%

Vignettes (2)

CNV HTML
intro HTML

How these are measured

Downloads

6.6K

CRAN downloads in the past year

Rank #7,396 · ~18/day · ~554/mo

Releases R versions

Daily download trend is not available in this view yet.

38830 days

1.2K90 days

6.6K1 year

Compare downloads with other packages →

Also on92 r2u

How downloads are counted

Repository

fumi-github/scploidy ↗Account: fumi-github

4Stars

2Forks

3Open issues

0Open PRs

0Releases

140Commits

1Commit identities

140 commits · Last activity 2024-07-03

Responsiveness

not measured

How these are measured

PracticesBeta

Checks run against github.com/fumi-github/scploidy on 2026-10-11.

No development-tooling practices detected in the upstream repository.

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Installing scPloidy adds 73 packages (40 with compiled code, 74 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB. 2 more not on CRAN are not measured.

Depends (1)

R >= 3.5.0

Imports (12)

dplyr GenomicRanges magrittrMASSmatrixStats mixtools nimble rlang Rsamtools tibble tidyrutils

LinkingTo (0)

none

Suggests (6)

gplots IRanges knitr readr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Fumihiko Takeuchi

Author, Maintainer since 0.3.0 (2022)

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.6.2Latest
record
2024-04-29 · current release · diff ↗ ·
added 1 export
cnv
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.3.0
record
2022-09-12
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-09-12
Total releases: 2 / 4 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Bundled data: 629 KB / 2 files
Download size: 3.1 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("scPloidy")

Format

Takeuchi, F. (2024). scPloidy: Infer Ploidy of Single Cells (Version 0.6.2) [Computer software]. https://doi.org/10.32614/CRAN.package.scPloidy

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 scPloidy version 0.6.2 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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