GenoPop

1.0.0

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

0packages depend

2.6Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by Marie GurkeFirst published 2024-09-112 releasesCRAN 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.

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

Health

CRAN checks

1NOTE12OK

Failing flavors

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

Slowest check: 7.8 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.04

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

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 · 711 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 99%
Return-value docs: 100%
References docs: 0%

Downloads

2.6K

CRAN downloads in the past year

Rank #18,384 · ~7/day · ~214/mo

Releases R versions

Daily download trend is not available in this view yet.

18830 days

59590 days

2.6K1 year

Compare downloads with other packages →

Also on98 r2u

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

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.

Code & Tests

People & History

People (1)

Maintainer (1)

Marie Gurke

Author, Maintainer

Authors (1)

Marie Gurke

Author, Maintainer

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
R
R 4.5.0 released · 2025-04-11
1.0.0Latest
2024-11-25 · current release · diff ↗
0.9.3
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
Installed size: not tracked yet
With dependencies: not tracked yet

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