tidypopgen: Tidy Population Genetics
We provide a tidy grammar of population genetics, facilitating the manipulation and analysis of data on biallelic single nucleotide polymorphisms (SNPs). 'tidypopgen' scales to very large genetic datasets by storing genotypes on disk, and performing operations on them in chunks, without ever loading all data in memory. The full functionalities of the package are described in Carter et al. (2025) <doi:10.1101/2025.06.06.658325>.
| Version: | 0.3.2 |
| Depends: | R (≥ 3.5.0), dplyr, tibble |
| Imports: | bigparallelr, bigsnpr, bigstatsr, foreach, generics, ggplot2, methods, MASS, patchwork, runner, rlang, sf, stats, tidyselect, tidyr, utils, Rcpp, UpSetR, vctrs |
| LinkingTo: | Rcpp, RcppArmadillo (≥ 0.9.600), bigstatsr, rmio |
| Suggests: | adegenet, admixtools, broom, data.table, hierfstat, knitr, detectRUNS, LEA, RhpcBLASctl, rmarkdown, rnaturalearth, rnaturalearthdata, readr, reticulate, testthat (≥ 3.0.0), vcfR, xgboost, spelling |
| Published: | 2025-08-27 |
| DOI: | 10.32614/CRAN.package.tidypopgen |
| Author: | Evie Carter [aut],
Eirlys Tysall [aut],
Andrea Manica 
[aut, cre, cph],
Chang Christopher [ctb] (Author of Hardy-Weinberg Equilibrium algorithm
in PLINK 1.90, used in loci_hwe()),
Shaun Purcell [ctb] (Author of Hardy-Weinberg Equilibrium algorithm in
PLINK 1.90, used in loci_hwe()),
Bengtsson Henrik [ctb] (Author of countLines in R.utils, modified for
.vcf in count_vcf_variants()) |
| Maintainer: | Andrea Manica <am315 at cam.ac.uk> |
| BugReports: | https://github.com/EvolEcolGroup/tidypopgen/issues |
| License: | GPL (≥ 3) |
| URL: | https://github.com/EvolEcolGroup/tidypopgen, https://evolecolgroup.github.io/tidypopgen/ |
| NeedsCompilation: | yes |
| Additional_repositories: | https://evolecolgroup.r-universe.dev/ |
| Language: | en-GB |
| Materials: | README, NEWS |
| CRAN checks: | tidypopgen results |
Documentation:
| Reference manual: | tidypopgen.html , tidypopgen.pdf |
| Vignettes: |
The grammar of population genetics (source, R code) Quality Control (source, R code) Population genetic analysis with tidypopgen (source, R code) PLINK cheatsheet (source, R code) tidypopgen (source, R code) |
Downloads:
| Package source: | tidypopgen_0.3.2.tar.gz |
| Windows binaries: | r-devel: not available, r-release: not available, r-oldrel: not available |
| macOS binaries: | r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): tidypopgen_0.3.2.tgz, r-oldrel (x86_64): tidypopgen_0.3.2.tgz |
Linking:
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