Package: PopGenHelpR 1.4.2

PopGenHelpR: Streamline Population Genomic and Genetic Analyses

Estimate commonly used population genomic statistics and generate publication quality figures. 'PopGenHelpR' uses vcf, 'geno' (012), and csv files to generate output.

Authors:Keaka Farleigh [aut, cph, cre], Mason Murphy [aut, cph, ctb], Christopher Blair [aut, cph, ctb], Tereza Jezkova [aut, cph, ctb]

PopGenHelpR_1.4.2.tar.gz
PopGenHelpR_1.4.2.zip(r-4.7)PopGenHelpR_1.4.2.zip(r-4.6)PopGenHelpR_1.4.2.zip(r-4.5)
PopGenHelpR_1.4.2.tgz(r-4.6-any)PopGenHelpR_1.4.2.tgz(r-4.5-any)
PopGenHelpR_1.4.2.tar.gz(r-4.7-any)PopGenHelpR_1.4.2.tar.gz(r-4.6-any)
PopGenHelpR_1.4.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PopGenHelpR/json (API)

# Install 'PopGenHelpR' in R:

install.packages('PopGenHelpR', repos = c('https://kfarleigh.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/kfarleigh/popgenhelpr/issues

Pkgdown/docs site:https://kfarleigh.github.io

Datasets:

Fst_dat - A genetic differentiation matrix and locality information for each population. This data was generated by subsetting data of Farleigh et al., 2021.
Het_dat - A data frame of hypothetical heterozygosity data produced by Heterozygosity.
HornedLizard_Pop - A population assignment data frame to be used in 'Heterozygosity' and 'Differentiation'.
HornedLizard_VCF - A vcfR object to be used in 'Heterozygosity' and 'Differentiation'.
Q_dat - A list representing a q-matrix and the locality information associated with the qmatrix

On CRAN:

diversity fst heterozygosity interpolation neis population-genetics population-genomics private-alleles snmf structure vcf

5.81 score 5 stars 16 scripts 572 downloads 10 exports 83 dependencies

Last updated from:ab298cbcd7. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	164
source / vignettes	OK	265
linux-release-x86_64	OK	169
macos-release-arm64	OK	110
macos-oldrel-arm64	OK	97
windows-devel	OK	120
windows-release	OK	104
windows-oldrel	OK	118
wasm-release	OK	136

Exports:Ancestry_barchart Differentiation Heterozygosity Network_map Pairwise_heatmap PCA Piechart_map Plot_coordinates Point_map Private.alleles

Dependencies:abind ape base64enc boot class classInt cli cluster cpp11 crayon curl DBI deldir digest dplyr e1071 farver fs generics geodata ggforce ggfun ggplot2 ggspatial glue gtable hms isoband jpeg jsonlite KernSmooth labeling lattice lifecycle magrittr MASS Matrix memuse mgcv nlme permute pillar pinfsc50 pkgconfig plyr png polyclip prettyunits progress proxy purrr R6 rappdirs RColorBrewer Rcpp reshape2 rlang rosm s2 S7 scales scatterpie sf sp spData spdep stringi stringr systemfonts terra tibble tidyr tidyselect tweenr units utf8 vcfR vctrs vegan viridisLite withr wk yulab.utils

PopGenHelpR Vignette

Rendered fromPopGenHelpR_vignette.Rmdusingknitr::rmarkdown

Last update: 2025-08-06
Started: 2023-02-03

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Plot an ancestry matrix for individuals and(or) populations.	Ancestry_barchart
A function to estimate three measures of genetic differentiation using geno files, vcf files, or vcfR objects. Data is assumed to be bi-allelic.	Differentiation
A genetic differentiation matrix and locality information for each population. This data was generated by subsetting data of Farleigh et al., 2021.	Fst_dat
A data frame of hypothetical heterozygosity data produced by Heterozygosity.	Het_dat
A function to estimate seven measures of heterozygosity using geno files, vcf files, or vcfR objects. Data is assumed to be bi-allelic.	Heterozygosity
A population assignment data frame to be used in 'Heterozygosity' and 'Differentiation'.	HornedLizard_Pop
A vcfR object to be used in 'Heterozygosity' and 'Differentiation'.	HornedLizard_VCF
A function to map statistics (i.e., genetic differentiation) between points as a network on a map.	Network_map
A function to plot a heatmap from a symmetric matrix.	Pairwise_heatmap
A function to perform principal component analysis (PCA) on genetic data. Loci with missing data will be removed prior to PCA.	PCA
Plot a map of ancestry pie charts.	Piechart_map
A function to plot coordinates on a map.	Plot_coordinates
A function to map statistics as colored points on a map.	Point_map
A function to estimate the number of private alleles in each population.	Private.alleles
A list representing a q-matrix and the locality information associated with the qmatrix	Q_dat