Package: pooledpeaks 1.0.6

Kathleen Kuesters

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>.

Authors:Kathleen Kuesters [aut, cre, cph], Jeffrey Long [aut], Jessica Blanton [aut], Walter Blank [ctb], Jeffrey Kovach [ctb], Ronald Blanton [ctb]

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pooledpeaks.pdf |pooledpeaks.html✨
pooledpeaks/json (API)
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Bug tracker:https://github.com/kmkuesters/pooledpeaks/issues

On CRAN:

25 exports 1.58 score 32 dependencies 1 scripts 85 downloads

Last updated 7 days agofrom:57da2fec3c. Checks:OK: 7. Indexed: yes.

Exports:AlRichassociate_dyesBootStrap3check_fsa_v_batchclean_scoresclusterClusterFromSamplesdata_manipulationDistCorEmpiricalSEfsa_batch_impfsa_metadataGeneIdentityMatrixGeneticDistanceMatrixGSTJostDlf_to_tdfLoadDataMDSplotPCDMRep_checkRWCDistanceMatrixscore_markers_rev3TwoLevelGSTTypedLoci

Dependencies:apeaskpassclicpp11curldigestdplyrfansiFragmangenericsgluelatticelifecyclemagrittrnlmepdftoolspillarpkgconfigpurrrqpdfR6Rcpprlangstringistringrsystibbletidyrtidyselectutf8vctrswithr