BIGr

0.7.2

Breeding Insight Genomics Functions for Polyploid and Diploid Species

0packages depend

3.2Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by Alexander M. SandercockFirst published 2025-05-193 releasesCRAN page ↗GitHub ↗

Functions developed within Breeding Insight to analyze diploid and polyploid breeding and genetic data. 'BIGr' provides the ability to filter variant call format (VCF) files, extract single nucleotide polymorphisms (SNPs) from diversity arrays technology missing allele discovery count (DArT MADC) files, and manipulate genotype data for both diploid and polyploid species. It also serves as the core dependency for the 'BIGapp' 'Shiny' app, which provides a user-friendly interface for performing routine genotype analysis tasks such as dosage calling, filtering, principal component analysis (PCA), genome-wide association studies (GWAS), and genomic prediction. For more details about the included 'breedTools' functions, see Funkhouser et al. (2017) <doi:10.2527/tas2016.0003>, and the 'updog' output format, see Gerard et al. (2018) <doi:10.1534/genetics.118.301468>.

Install

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

install.packages("BIGr")

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

pak::pak("Breeding-Insight/BIGr")

Development version from Breeding-Insight/BIGr. Requires the pak package.

Release

# one-time r2u setup for Ubuntu (noble)

curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash

# then install

sudo apt install r-cran-bigr

Fast Ubuntu binaries via r2u (no compilation). Run the setup once per machine.

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

Health

CRAN checks

1ERROR12OK

Failing flavors

ERROR r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 0.56

not tracked

Coverage

100%

Documentation · exports

None

Vignettes

Yes

README

Dependencies · direct

Check history

ERROR2026-03-10
11 OK · 0 NOTE · 0 WARNING · 3 ERROR · 0 FAILURE

Downloads

3.2K

CRAN downloads in the past year

Rank #10,668 · ~9/day · ~267/mo

Releases R versions

BIGr

Daily download trend is not available in this view yet.

Compare downloads with other packages →

45930 days

1K90 days

3.2K1 year

Also on213 r2u

Source & community

GitHub ↗

Repository stars, issues, and contributor activity are not tracked yet.

Dependencies

Declared dependencies

23 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.4.0

Imports (16)

parallel basedplyr Rdpack readr reshape2 rlang tidyr vcfR Rsamtools Biostrings pwalign janitor quadprog tibble stringr data.table

LinkingTo (0)

none

Suggests (8)

covr ggplot2 spelling rmdformats knitr rmarkdown polyRAD testthat

Enhances (0)

none

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code

11,038Lines of code

24Exported functions

Code & tests

Open call graph →

Line coverage

–

Expression

–

Tests / Examples

–

Functions

37 24 exported

Complexity

14.4 avg / 63 max

Call network

37 nodes / 28 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (8)

Maintainer (1)

Alexander M. Sandercock

Maintainer, Author

Authors (2)

Josue Chinchilla-Vargas

Author

Cristiane Taniguti

Author

Contributors (4)

Contributor

Contributor

Contributor

Contributor

University of Florida

Release timeline

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

0.7.2Latest
2026-05-18 · current release
R
R 4.6.0 released · 2026-04-24
0.6.2
2025-09-18 · diff ↗
0.5.5
2025-05-19

Package metadata

First published: 2025-05-19
Total releases: 3 / 1 yrs
License: Apache License (>= 2)
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet