R Observatory: Metrics for copyseparator version 1.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

copyseparator

1.2.0

Assembling Long Gene Copies from Short Read Data

0packages depend

2.7Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Lei YangFirst published 2022-05-243 releasesCRAN page ↗GitHub ↗

Assembles two or more gene copies from short-read Next-Generation Sequencing data. Works best when there are only two gene copies and read length >=250 base pairs. High and relatively even coverage are important.

Install

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

install.packages("copyseparator", 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("LeiYang-Fish/copyseparator")

Development version from LeiYang-Fish/copyseparator. 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-copyseparator

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

Slowest check: 3.2 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

11

Dependencies · direct

Check history

NOTE2026-08-09
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-08-02
10 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

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

Downloads

2.7K

CRAN downloads in the past year

Rank #14,565 · ~7/day · ~225/mo

Releases R versions

Daily download trend is not available in this view yet.

17230 days

72790 days

2.7K1 year

Compare downloads with other packages →

Also on113 r2u

Repository

GitHub ↗ leiyang-fish/copyseparator

0Stars

0Forks

0Open issues

0Open PRs

0Releases

Last activity 2024-12-23

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/leiyang-fish/copyseparator on 2026-08-23.

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (11)

ape seqinr stringr kmer DECIPHER beepr BiostringsgrDevicesdoParallel foreachparallel

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (0)

Author records are not tracked yet for this package.

Listed in earlier versions (1)

Lei Yang

no longer listed · 1.0.0 to 1.2.0

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.2.0Latest
2022-11-25 · current release · diff ↗
1.1.0
2022-07-06 · diff ↗
1.0.0
2022-05-24
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-05-24
Total releases: 3 / 4 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.5.0
Download size: 98 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("copyseparator")

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 copyseparator version 1.2.0 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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