R Observatory: Metrics for karyotapR version 1.0.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

karyotapR

1.0.2Package record

DNA Copy Number Analysis for Genome-Wide Tapestri Panels

0packages depend

3.2Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Joseph MaysCRAN page ↗GitHub ↗Website ↗Issues ↗

Analysis of DNA copy number in single cells using custom genome-wide targeted DNA sequencing panels for the Mission Bio Tapestri platform. Users can easily parse, manipulate, and visualize datasets produced from the automated 'Tapestri Pipeline', with support for normalization, clustering, and copy number calling. Functions are also available to deconvolute multiplexed samples by genotype and parsing barcoded reads from exogenous lentiviral constructs.

Changes in 1.0.2

Patched to handle tests failing to load GenomeInfoDb package dependency.

From NEWS.md in the release

Install

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

install.packages("karyotapR", 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("joeymays/karyotapR")

Development version from joeymays/karyotapR. 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-karyotapr

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:
  ‘GenomeInfoDb’
All declared Imports should be used.

CRAN check page ↗

Slowest check: 7.7 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTE2026-09-24
ERROR10 OK, 2 NOTE, 1 ERROR2026-09-17
NOTE11 OK, 2 NOTE2026-05-10
ERROR10 OK, 2 NOTE, 1 ERROR2026-05-03
NOTE12 OK, 2 NOTE2026-03-16

Show 2 earlier changesHide 2 earlier changes

ERROR12 OK, 1 NOTE, 1 ERROR2026-03-13
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.2

READMEYes · 166 wordsVignettesNoNEWSYes · 100% structured · mentions 1.0.2Citation fileNoWebsiteYes · pkgdown

The repository also keeps web-only articles.

Help pages: 25 (1 internal)includes a package overview page
Examples that run: 79%19 run in a plain check · 3 only when donttest examples are enabled (R CMD check --as-cran) · 2 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

3.2K

CRAN downloads in the past year

Rank #8,944 · ~9/day · ~263/mo

Releases R versions

Daily download trend is not available in this view yet.

36930 days

1K90 days

3.2K1 year

Compare downloads with other packages →

Also on88 r2u

How downloads are counted

Repository

joeymays/karyotapr ↗Account: joeymays

1Stars

1Forks

0Open issues

0Open PRs

3Releases

228Commits

1Commit identities

228 commits · Last activity 2025-11-02

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 2
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2024-08-04 · 12026-07-07 · 1

How these are measured

PracticesBeta

8 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/joeymays/karyotapr on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2025-11-02 · The repository has a site deploy workflow

pkgdown site last built 2025-11-02

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

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

Dependencies

Declared dependencies

27 external dependencies (excludes base and recommended)

Installing karyotapR adds 50 packages (30 with compiled code, 48 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, dbscan 3.8 MB. 8 more not on CRAN are not measured.

Depends (2)

R >= 4.1SingleCellExperiment

Imports (23)

circlize cli ComplexHeatmap dbscan dplyr fitdistrplus GenomeInfoDb GenomicRanges ggplot2 gtools IRanges magrittrmethodspurrr rhdf5 rlang S4VectorsstatsSummarizedExperiment tibble tidyr umap viridisLite

LinkingTo (0)

none

Suggests (5)

Biostrings knitr rmarkdown Rsamtools testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (1)

Joseph Mays

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.0.2Latest
record
2025-11-01 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0.1
record
2023-09-07
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-09-07
Total releases: 2 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1
Download size: 1.1 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("karyotapR")

Format

Mays, J. (2025). karyotapR: DNA Copy Number Analysis for Genome-Wide Tapestri Panels (Version 1.0.2) [Computer software]. https://doi.org/10.32614/CRAN.package.karyotapR

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 karyotapR version 1.0.2 [Data set]. HJJB, LLC. Data release v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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