pooledpeaks: Genetic Analysis of Pooled Samples
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:
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