R Observatory: Metrics for findGSEP version 1.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

findGSEP

1.2.0

Estimate Genome Size of Polyploid Species Using k-Mer Frequencies

0packages depend

2.1Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Laiyi FuFirst published 2024-05-261 releasesCRAN page ↗GitHub ↗

Provides tools to estimate the genome size of polyploid species using k-mer frequencies. This package includes functions to process k-mer frequency data and perform genome size estimation by fitting k-mer frequencies with a normal distribution model. It supports handling of complex polyploid genomes and offers various options for customizing the estimation process. The basic method 'findGSE' is detailed in Sun, Hequan, et al. (2018) doi:10.1093/bioinformatics/btx637.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("findGSEP", 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("sperfu/findGSEP")

Development version from sperfu/findGSEP. 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-findgsep

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

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-findGSEP

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-findGSEP

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 2.0 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

6

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 628 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 81%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.1K

CRAN downloads in the past year

Rank #21,486 · ~6/day · ~177/mo

Releases R versions

Daily download trend is not available in this view yet.

15330 days

51090 days

2.1K1 year

Compare downloads with other packages →

Also on96 r2u18 autocran

Repository

GitHub ↗ sperfu/findgsep

9Stars

3Forks

3Open issues

0Open PRs

0Releases

32Commits

1Contributors

32 commits · Last activity 2024-07-27 · 0% stars, 30d

Stars over time

2025-04-20 · 52026-07-07 · 9

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/sperfu/findgsep on 2026-08-16.

Continuous integration (1)

GitHub Actions

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (4)

R >= 4.2.0RColorBrewer ggplot2grDevices

Imports (3)

pracma scales dplyr

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Laiyi Fu

Author, Maintainer

Authors (2)

Laiyi Fu

Author, Maintainer

Hequan Sun

Author

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.2.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2024-05-26
Total releases: 1 / 2 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.2.0
Download size: 97 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("findGSEP")

Format

Fu, L., & Sun, H. (2024). findGSEP: Estimate Genome Size of Polyploid Species Using k-Mer Frequencies (Version 1.2.0) [Computer software]. https://doi.org/10.32614/CRAN.package.findGSEP

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 findGSEP version 1.2.0 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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