BIGr: Breeding Insight Genomics Functions for Polyploid and Diploid
Species
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 |
| 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 |
Documentation:
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