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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", "2.9.7")



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: 2023-06-07
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 2.9.7, https://cran.r-project.org/web/packages/dartR. Accessed 19 Feb. 2025.
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
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