Other packages > Find by keyword >

dartR  

Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis
View on CRAN: Click here


Download and install dartR package within the R console
Install from CRAN:
install.packages("dartR")

Install from Github:
library("remotes")
install_github("cran/dartR")

Install by package version:
library("remotes")
install_version("dartR", "2.9.9.5")



Attach the package and use:
library("dartR")
Maintained by
Bernd Gruber
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2017-06-23
Latest Update: 2025-03-25
Description:
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.
How to cite:
Bernd Gruber (2017). dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis. R package version 2.9.9.5, https://cran.r-project.org/web/packages/dartR. Accessed 04 Jun. 2026.
Previous versions and publish date:
0.79 (2017-06-23 08:38), 0.80 (2017-06-23 18:00), 0.91 (2017-08-15 14:18), 0.93 (2017-08-21 12:22), 1.0.5 (2018-05-11 09:25), 1.0 (2017-12-06 12:25), 1.1.6 (2018-11-26 06:20), 1.1.11 (2019-02-07 15:13), 1.8.3 (2020-09-01 13:40), 1.9.1 (2021-04-03 15:50), 1.9.4 (2021-04-08 08:10), 1.9.6 (2021-04-30 08:50), 1.9.9.1 (2021-05-28 19:10), 2.0.3 (2022-03-28 16:50), 2.0.4 (2022-06-05 18:00), 2.7.2 (2022-12-06 11:20), 2.9.7 (2023-06-07 12:40)
Other packages that cited dartR R package
View dartR citation profile
Other R packages that dartR depends, imports, suggests or enhances
Complete documentation for dartR
Functions, R codes and Examples using the dartR R package
Some associated functions: bandicoot.gl . cbind.dartR . gi2gl . gl.He . gl.Ho . gl.LDNe . gl.alf . gl.amova . gl.assign.grm . gl.assign.mahalanobis . gl.assign.pa . gl.assign.pca . gl.basic.stats . gl.blast . gl.check.verbosity . gl.collapse . gl.compliance.check . gl.costdistances . gl.define.pop . gl.diagnostics.hwe . gl.diagnostics.sim . gl.dist.ind . gl.dist.pop . gl.drop.ind . gl.drop.loc . gl.drop.pop . gl.edit.recode.ind . gl.edit.recode.pop . gl.evanno . gl.fdsim . gl.filter.allna . gl.filter.callrate . gl.filter.hamming . gl.filter.heterozygosity . gl.filter.hwe . gl.filter.ld . gl.filter.locmetric . gl.filter.maf . gl.filter.monomorphs . gl.filter.overshoot . gl.filter.pa . gl.filter.parent.offspring . gl.filter.rdepth . gl.filter.reproducibility . gl.filter.secondaries . gl.filter.sexlinked . gl.filter.taglength . gl.fixed.diff . gl.fst.pop . gl.genleastcost . gl.grm.network . gl.grm . gl.hwe.pop . gl.ibd . gl.impute . gl.install.vanilla.dartR . gl.join . gl.keep.ind . gl.keep.loc . gl.keep.pop . gl.ld.distance . gl.ld.haplotype . gl.list.reports . gl.load . gl.make.recode.ind . gl.make.recode.pop . gl.map.interactive . gl.map.structure . gl.merge.pop . gl.nhybrids . gl.outflank . gl.pcoa . gl.pcoa.plot . gl.percent.freq . gl.play.history . gl.plot.heatmap . gl.plot.network . gl.plot.structure . gl.print.history . gl.print.reports . gl.propShared . gl.random.snp . gl.read.csv . gl.read.dart . gl.read.fasta . gl.read.silicodart . gl.read.vcf . gl.reassign.pop . gl.recalc.metrics . gl.recode.ind . gl.recode.pop . gl.rename.pop . gl.report.bases . gl.report.callrate . gl.report.diversity . gl.report.hamming . gl.report.heterozygosity . gl.report.hwe . gl.report.ld.map . gl.report.ld . gl.report.locmetric . gl.report.maf . gl.report.monomorphs . gl.report.overshoot . gl.report.pa . gl.report.parent.offspring . gl.report.rdepth . gl.report.reproducibility . gl.report.secondaries . gl.report.sexlinked . gl.report.taglength . gl.run.structure . gl.sample . gl.save . gl.select.colors . gl.select.shapes . gl.set.verbosity . gl.sfs . gl.sim.WF.run . gl.sim.WF.table . gl.sim.create_dispersal . gl.sim.emigration . gl.sim.ind . gl.sim.mutate . gl.sim.offspring . gl.smearplot . gl.sort . gl.spatial.autoCorr . gl.subsample.loci . gl.test.heterozygosity . gl.tree.nj . gl.write.csv . gl2bayescan . gl2bpp . gl2demerelate . gl2eigenstrat . gl2fasta . gl2faststructure . gl2gds . gl2genalex . gl2genepop . gl2geno . gl2gi . gl2hiphop . gl2phylip . gl2plink . gl2related . gl2sa . gl2sfs . gl2shp . gl2snapp . gl2structure . gl2svdquartets . gl2treemix . gl2vcf . interactive_reference . interactive_sim_run . is.fixed . platy . possums.gl . rbind.dartR . sub-dartR-ANY-ANY-ANY-method . testset.gl . testset.gs . testset_SNPs_2Row . testset_metadata . testset_pop_recode . theme_dartR . utils.assignment . utils.assignment_2 . utils.assignment_3 . utils.assignment_4 . utils.basic.stats . utils.check.datatype . utils.dart2genlight . utils.dist.binary . utils.dist.ind.snp . utils.flag.start . utils.hamming . utils.het.pop . utils.jackknife . utils.n.var.invariant . utils.outflank.MakeDiploidFSTMat . utils.outflank . utils.outflank.plotter . utils.read.dart . utils.recalc.avgpic . utils.recalc.callrate . utils.recalc.freqhets . utils.recalc.freqhomref . utils.recalc.freqhomsnp . utils.recalc.maf . utils.reset.flags . utils.spautocor . utils.structure.evanno . utils.structure.genind2gtypes . utils.structure.run . zzz . 
Some associated R codes: gi2gl.R . gl.sfs.R . gl2sfs.R . gl2shp.R . utils.check.datatype.R . utils.impute.R . utils.jackknife.R . utils.spautocor.R . utils.transpose.R .  Full dartR package functions and examples
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

murphydiagram  
Murphy Diagrams for Forecast Comparisons
Data and code for the paper by Ehm, Gneiting, Jordan and Krueger ('Of Quantiles and Expectiles: Con ...
Download / Learn more Package Citations See dependency  
shinybusy  
Busy Indicators and Notifications for 'Shiny' Applications
Add indicators (spinner, progress bar, gif) in your 'shiny' applications to show the user that the ...
Download / Learn more Package Citations See dependency  
nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  
golem  
A Framework for Robust Shiny Applications
An opinionated framework for building a production-ready 'Shiny' application. This package contains ...
Download / Learn more Package Citations See dependency  
AMPLE  
Shiny Apps to Support Capacity Building on Harvest Control Rules
Three Shiny apps are provided that introduce Harvest Control Rules (HCR) for fisheries management. ...
Download / Learn more Package Citations See dependency  
crplyr  
A 'dplyr' Interface for Crunch
In order to facilitate analysis of datasets hosted on the Crunch data platform ...
Download / Learn more Package Citations See dependency  

27,268

R Packages

233,548

Dependencies

72,590

Author Associations

27,205

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA