CRAN/E | dartR

dartR

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

Installation

About

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.

Citation dartR citation info
green-striped-gecko.github.io/dartR/
Bug report File report

Key Metrics

Version 2.9.7
R ≥ 3.5
Published 2023-06-07 296 days ago
Needs compilation? no
License GPL (≥ 3)
CRAN checks dartR results

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Maintainer

Maintainer

Bernd Gruber

bernd.gruber@canberra.edu.au

Authors

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

Material

Reference manual
Package source

Vignettes

dartR_Tutorials

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

dartR archive

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 ≥ 1.6.1
StAMPP
stats
stringr
tidyr
utils
vegan

Suggests

boot
devtools
directlabels
dismo
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expm
gdistance
ggtern
gganimate
ggrepel
grid
gtable
ggthemes
gplots
HardyWeinberg
hierfstat
igraph
iterpc
knitr
label.switching
lattice
leaflet
leaflet.minicharts
markdown
mmod
networkD3
parallel
pegas
pheatmap
plotly
poppr
proxy
purrr
qvalue
RColorBrewer
Rcpp
rgl
rmarkdown
rrBLUP
scales
seqinr
shinyBS
shinyjs
shinythemes
shinyWidgets
SIBER
snpStats
stringi
terra
tibble
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Reverse Imports

PopGenHelpR