pooledpeaks: Genetic Analysis of Pooled Samples (original) (raw)

Analyzing genetic data obtained from pooled samples. This package can read in Fragment Analysis output files, process the data, and score peaks, as well as facilitate various analyses, including cluster analysis, calculation of genetic distances and diversity indices, as well as bootstrap resampling for statistical inference. Specifically tailored to handle genetic data efficiently, researchers can explore population structure, genetic differentiation, and genetic relatedness among samples. We updated some functions from Covarrubias-Pazaran et al. (2016) <doi:10.1186/s12863-016-0365-6> to allow for the use of new file formats and referenced the following to write our genetic analysis functions: Long et al. (2022) <doi:10.1038/s41598-022-04776-0>, Jost (2008) <doi:10.1111/j.1365-294x.2008.03887.x>, Nei (1973) <doi:10.1073/pnas.70.12.3321>, Foulley et al. (2006) <doi:10.1016/j.livprodsci.2005.10.021>, Chao et al. (2008) <doi:10.1111/j.1541-0420.2008.01010.x>.

Version:	1.2.2
Imports:	ape, dplyr, Fragman, graphics, magrittr, pdftools, qpdf, rlang, stats, tibble, tidyr, utils
Suggests:	knitr, plyr, rmarkdown, testthat (≥ 3.0.0)
Published:	2025-05-09
DOI:	10.32614/CRAN.package.pooledpeaks
Author:	Kathleen Kuesters [aut, cre, cph], Jeffrey Long [aut], Jessica Blanton [aut], Walter Blank [ctb], Jeffrey Kovach [ctb], Ronald Blanton [ctb]
Maintainer:	Kathleen Kuesters <kathleen.kuesters at gmail.com>
BugReports:	https://github.com/kmkuesters/pooledpeaks/issues
License:	GPL (≥ 3)
URL:	https://github.com/kmkuesters/pooledpeaks
NeedsCompilation:	no
Materials:	README, NEWS
CRAN checks:	pooledpeaks results

Documentation:

Downloads:

Linking:

Please use the canonical formhttps://CRAN.R-project.org/package=pooledpeaksto link to this page.