karyotapR

1.0.2

DNA Copy Number Analysis for Genome-Wide Tapestri Panels

0packages depend

2.8Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Joseph MaysFirst published 2023-09-072 releasesCRAN page ↗GitHub ↗

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.

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.

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

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc

Slowest check: 9.8 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.01

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-05-10
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-03
10 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-16
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-13
12 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 166 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 83%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.8K

CRAN downloads in the past year

Rank #15,435 · ~8/day · ~229/mo

Releases R versions

Daily download trend is not available in this view yet.

23330 days

69990 days

2.8K1 year

Compare downloads with other packages →

Also on122 r2u

Repository

GitHub ↗ joeymays/karyotapr

1Stars

1Forks

0Open issues

0Open PRs

3Releases

228Commits

1Contributors

228 commits · Last activity 2025-11-02

Stars over time

2024-08-04 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/joeymays/karyotapr on 2026-07-26.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

27 external dependencies (excludes base and recommended)

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.

Code & Tests

People & History

People (1)

Maintainer (1)

Joseph Mays

Author, Maintainer, Copyright holder

Authors (1)

Joseph Mays

Author, Maintainer, Copyright holder

Joseph Mays

Author, Maintainer, Copyright holder

Package Timeline

2 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.2Latest
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
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
Installed size: not tracked yet
With dependencies: not tracked yet

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