genio

1.1.2

Genetics Input/Output Functions

5packages depend

18.6Kdownloads / year

89.4%test coverage

13/13checks pass

Overview

About

Maintained by Alejandro OchoaFirst published 2019-05-247 releasesCRAN page ↗GitHub ↗

Implements readers and writers for file formats associated with genetics data. Reading and writing Plink BED/BIM/FAM and GCTA binary GRM formats is fully supported, including a lightning-fast BED reader and writer implementations. Other functions are 'readr' wrappers that are more constrained, user-friendly, and efficient for these particular applications; handles Plink and Eigenstrat tables (FAM, BIM, IND, and SNP files). There are also make functions for FAM and BIM tables with default values to go with simulated genotype data.

Install

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

install.packages("genio", 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("OchoaLab/genio")

Development version from OchoaLab/genio. 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-genio

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

# 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-genio

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

Health

CRAN checks

13OK

Slowest check: 2.4 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 4.11

89.4%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 180 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 97%
References docs: 0%

Downloads

18.6K

CRAN downloads in the past year

Rank #3,459 · ~51/day · ~1.5K/mo

Releases R versions

Daily download trend is not available in this view yet.

89930 days

3.2K90 days

18.6K1 year

Compare downloads with other packages →

Also on475 r2u27 autocran2.4K conda_forge

Repository

GitHub ↗ ochoalab/genio

19Stars

3Forks

3Open issues

1Open PRs

7Releases

104Commits

1Contributors

License GPL-3.0 · 104 commits · Last activity 2025-02-20 · 0% stars, 30d

Stars over time

2025-03-01 · 182026-07-07 · 19

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/ochoalab/genio on 2026-07-26.

CRAN release process (1)

cran-comments.md

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

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (4)

readr tibble dplyr Rcpp

LinkingTo (1)

Rcpp

Suggests (6)

testthat knitr rmarkdown BEDMatrix snpStats lobstr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

5direct

0indirect

jackstraw lit modACDC smer MoBPS

Code & Tests

People & History

People (1)

Maintainer (1)

Alejandro Ochoa

Author, Maintainer

Authors (1)

Alejandro Ochoa

Author, Maintainer

Package Timeline

7 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
1.1.2Latest
2023-01-07 · current release · diff ↗
1.1.1
2022-04-27 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.25
2021-07-27 · diff ↗
1.0.23
2021-06-11 · diff ↗
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
1.0.12
2019-12-18 · diff ↗
1.0.10
2019-05-28 · diff ↗
1.0.9
2019-05-24
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-05-24
Total releases: 7 / 7 yrs
License: GPL-3 OSI
Download size: 570 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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