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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>.
| Version: | 0.5.5 |
| Depends: | R (≥ 4.4.0) |
| Imports: | parallel, dplyr, Rdpack (≥ 0.7), readr (≥ 2.1.5), reshape2 (≥ 1.4.4), tidyr (≥ 1.3.1), vcfR (≥ 1.15.0), Rsamtools, Biostrings, pwalign, janitor, quadprog, tibble |
| Suggests: | covr, spelling, rmdformats, knitr (≥ 1.10), rmarkdown, testthat (≥ 3.0.0) |
| Published: | 2025-05-19 |
| DOI: | 10.32614/CRAN.package.BIGr |
| Author: | Alexander M. Sandercock [cre, aut], Cristiane Taniguti [aut], Josue Chinchilla-Vargas [aut], Shufen Chen [ctb], Manoj Sapkota [ctb], Meng Lin [ctb], Dongyan Zhao [ctb], Cornell University [cph] (Breeding Insight) |
| Maintainer: | Alexander M. Sandercock <ams866 at cornell.edu> |
| BugReports: | https://github.com/Breeding-Insight/BIGr/issues |
| License: | Apache License (≥ 2) |
| URL: | https://github.com/Breeding-Insight/BIGr |
| NeedsCompilation: | no |
| Citation: | BIGr citation info |
| Materials: | README NEWS |
| CRAN checks: | BIGr results |
| Reference manual: | BIGr.pdf |
| Package source: | BIGr_0.5.5.tar.gz |
| Windows binaries: | r-devel: BIGr_0.5.5.zip, r-release: BIGr_0.5.5.zip, r-oldrel: not available |
| macOS binaries: | r-release (arm64): not available, r-oldrel (arm64): BIGr_0.5.5.tgz, r-release (x86_64): not available, r-oldrel (x86_64): not available |
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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.