Package: BIGpopA 1.0.5

Josue Chinchilla-Vargas

BIGpopA: Pedigree Validation Genetic Composition of Diploids & Polyploids

Tools for pedigree quality control and genomic breed/line composition estimation in diploid and polyploid breeding populations. 'BIGpopA' provides functions to check and correct common pedigree errors, assign parentage from SNP genotype data using Mendelian error rates, validate parent-offspring trios, and estimate genome-wide breed or line composition using quadratic programming. Supports both diploid and polyploid species. For more details about the included 'breedTools' functions, see Funkhouser et al. (2017) <doi:10.2527/tas2016.0003>.

Authors:Josue Chinchilla-Vargas [cre, aut], Alexander Sandercock [aut], University of Florida [cph]

BIGpopA_1.0.5.tar.gz
BIGpopA_1.0.5.zip(r-4.7)BIGpopA_1.0.5.zip(r-4.6)BIGpopA_1.0.5.zip(r-4.5)
BIGpopA_1.0.5.tgz(r-4.6-any)BIGpopA_1.0.5.tgz(r-4.5-any)
BIGpopA_1.0.5.tar.gz(r-4.7-any)BIGpopA_1.0.5.tar.gz(r-4.6-any)
BIGpopA_1.0.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BIGpopA/json (API)

# Install 'BIGpopA' in R:
install.packages('BIGpopA', repos = c('https://breeding-insight.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/breeding-insight/bigpopa/issues

On CRAN:

Conda:

3.18 score 3 scripts 5 exports 36 dependencies

Last updated from:d4f66aa1eb. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK152
source / vignettesOK190
linux-release-x86_64OK160
macos-release-arm64OK88
macos-oldrel-arm64OK102
windows-develOK88
windows-releaseOK91
windows-oldrelOK94
wasm-releaseOK130

Exports:allele_freq_polycheck_pedfind_parentagesolve_composition_polyvalidate_pedigree

Dependencies:clicpp11data.tabledplyrfarvergenericsggplot2gluegtablehmsisobandjanitorlabelinglifecyclelubridatemagrittrpillarpkgconfigpurrrquadprogR6RColorBrewerrlangS7scalessnakecasestringistringrtibbletidyrtidyselecttimechangeutf8vctrsviridisLitewithr