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

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>.

Version: 1.0.0
Imports: Rsamtools, GenomicRanges, foreach, doParallel, parallel, missForest, IRanges
Suggests: knitr, rmarkdown, testthat (≥ 3.0.0), withr
Published: 2024-11-25
DOI: 10.32614/CRAN.package.GenoPop
Author: Marie Gurke ORCID iD [aut, cre]
Maintainer: Marie Gurke <margurke at gmail.com>
License: GPL (≥ 3)
NeedsCompilation: no
Citation: GenoPop citation info
Materials: README
CRAN checks: GenoPop results

Documentation:

Reference manual: GenoPop.pdf
Vignettes: GenoPop (source, R code)

Downloads:

Package source: GenoPop_1.0.0.tar.gz
Windows binaries: r-devel: GenoPop_1.0.0.zip, r-release: GenoPop_1.0.0.zip, r-oldrel: GenoPop_1.0.0.zip
macOS binaries: r-release (arm64): GenoPop_1.0.0.tgz, r-oldrel (arm64): GenoPop_1.0.0.tgz, r-release (x86_64): GenoPop_1.0.0.tgz, r-oldrel (x86_64): GenoPop_1.0.0.tgz
Old sources: GenoPop archive

Linking:

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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.