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 Documentation: Downloads: Linking:Please use the canonical form https://CRAN.R-project.org/package=BIGr to link to this page.
RetroSearch is an open source project built by @garambo | Open a GitHub Issue
Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo
HTML:
3.2
| Encoding:
UTF-8
| Version:
0.7.4