R Observatory: Metrics for GenoPop version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

GenoPop

1.0.0Package record

Genotype Imputation and Population Genomics Efficiently from Variant Call Formatted (VCF) Files

0packages depend

2.7Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Marie GurkeCRAN page ↗

Tools for efficient processing of large, whole genome genotype data sets in variant call format (VCF). It includes several functions to calculate commonly used population genomic metrics and a method for reference panel free genotype imputation, which is described in the preprint Gurke & Mayer (2024) doi:10.22541/au.172515591.10119928/v1.

Install

R (CRAN)Ubuntu (r2u)

install.packages("GenoPop", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-genopop

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: 7.9 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.0

READMEYes · 711 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileYes · software entry onlyWebsitenot declared in DESCRIPTION

Help pages: 15 (2 internal)
Examples that run: 0%13 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 87%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

GenoPop HTML

How these are measured

Downloads

2.7K

CRAN downloads in the past year

Rank #12,715 · ~7/day · ~224/mo

Releases R versions

Daily download trend is not available in this view yet.

34030 days

88590 days

2.7K1 year

Compare downloads with other packages →

Also on71 r2u

How downloads are counted

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Installing GenoPop adds 14 packages (6 with compiled code, 6.3 MB of source tarballs). Heaviest: Rcpp 1.8 MB, RcppEigen 1.7 MB, rbibutils 1.1 MB. 3 more not on CRAN are not measured.

Depends (0)

none

Imports (7)

Rsamtools GenomicRanges foreach doParallelparallelmissForest IRanges

LinkingTo (0)

none

Suggests (4)

knitr rmarkdown testthat withr

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)

Marie Gurke

Author, Maintainer since 0.9.3 (2024)

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
1.0.0Latest
record
2024-11-25 · current release · diff ↗
0.9.3
record
2024-09-11
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-09-11
Total releases: 2 / 2 yrs
License: GPL (>= 3) OSI
Download size: 40 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("GenoPop")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.22541/au.172515591.10119928/v1.

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 GenoPop version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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