dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Functions are provided that facilitate the import and analysis of 'SNP' (single nucleotide polymorphism) and 'silicodart' (presence/absence) data. The main focus is on data generated by 'DarT' (Diversity Arrays Technology), however, data from other sequencing platforms can be used once 'SNP' or related fragment presence/absence data from any source is imported. Genetic datasets are stored in a derived 'genlight' format (package 'adegenet'), that allows for a very compact storage of data and metadata. Functions are available for importing and exporting of 'SNP' and 'silicodart' data, for reporting on and filtering on various criteria (e.g. 'CallRate', heterozygosity, reproducibility, maximum allele frequency). Additional functions are available for visualization (e.g. Principle Coordinate Analysis) and creating a spatial representation using maps. 'dartR' supports also the analysis of 3rd party software package such as 'newhybrid', 'structure', 'NeEstimator' and 'blast'. Since version 2.0.3 we also implemented simulation functions, that allow to forward simulate 'SNP' dynamics under different population and evolutionary dynamics. Comprehensive tutorials and support can be found at our 'github' repository: github.com/green-striped-gecko/dartR/. If you want to cite 'dartR', you find the information by typing citation('dartR') in the console.

Version: 2.7.2
Depends: R (≥ 3.5), adegenet (≥ 2.0.0), ggplot2, dplyr, dartR.data
Imports: ape, crayon, data.table, fields, foreach, gridExtra, MASS, methods, patchwork, plyr, PopGenReport, raster, reshape2, shiny, SNPRelate, sp, StAMPP, stats, stringr, tidyr, utils, vegan
Suggests: boot, devtools, directlabels, dismo, doParallel, expm, gdistance, ggtern, gganimate, ggrepel, grid, gtable, ggthemes, gplots, HardyWeinberg, hierfstat, igraph, iterpc, knitr, label.switching, lattice, leaflet, leaflet.minicharts, maptools, markdown, mmod, networkD3, parallel, pca3d, pegas, pheatmap, plotly, poppr, proxy, purrr, qvalue, RColorBrewer, Rcpp, rgl, rmarkdown, rrBLUP, scales, seqinr, shinyBS, shinyjs, shinythemes, shinyWidgets, SIBER, snpStats, stringi, terra, tibble, tidyverse, vcfR, zoo, viridis
Published: 2022-12-06
Author: Bernd Gruber [aut, cre], Arthur Georges [aut], Jose L. Mijangos [aut], Carlo Pacioni [aut], Peter J. Unmack [ctb], Oliver Berry [ctb], Lindsay V. Clark [ctb], Floriaan Devloo-Delva [ctb], Eric Archer [ctb]
Maintainer: Bernd Gruber <bernd.gruber at canberra.edu.au>
BugReports: https://groups.google.com/g/dartr?pli=1
License: GPL (≥ 3)
URL: https://green-striped-gecko.github.io/dartR/
NeedsCompilation: no
Citation: dartR citation info
CRAN checks: dartR results

Documentation:

Reference manual: dartR.pdf
Vignettes: dartR_Tutorials

Downloads:

Package source: dartR_2.7.2.tar.gz
Windows binaries: r-devel: dartR_2.7.2.zip, r-release: dartR_2.7.2.zip, r-oldrel: not available
macOS binaries: r-release (arm64): dartR_2.7.2.tgz, r-oldrel (arm64): dartR_2.7.2.tgz, r-release (x86_64): dartR_2.7.2.tgz, r-oldrel (x86_64): dartR_2.7.2.tgz
Old sources: dartR archive

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