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 15 Jul. 2026.
Previous versions and publish date:
(2026-07-09 07:30), 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

r2resize  
In-Text Resize for Images, Tables and Fancy Resize Containers in 'shiny', 'rmarkdown' and 'quarto' Documents
Automatic resizing toolbar for containers, images and tables. Various resizable or expandable contai ...
Download / Learn more Package Citations See dependency  
gscaLCA  
Generalized Structure Component Analysis- Latent Class Analysis & Latent Class Regression
Execute Latent Class Analysis (LCA) and Latent Class Regression (LCR) by using Generalized Structu ...
Download / Learn more Package Citations See dependency  
binhf  
Haar-Fisz Functions for Binomial Data
Binomial Haar-Fisz transforms for Gaussianization as in Nunes and Nason (2009). ...
Download / Learn more Package Citations See dependency  
SECFISH  
Disaggregate Variable Costs
These functions were developed within SECFISH project (Strengthening regional cooperation in the are ...
Download / Learn more Package Citations See dependency  
footBayes  
Fitting Bayesian and MLE Football Models
This is the first package allowing for the estimation, visualization and prediction of the most wel ...
Download / Learn more Package Citations See dependency  
pulseTD  
Identification of Transcriptional Dynamics using Pulse Models via 4su-Seq Data and RNA-Seq Data
A tool for analyzing the transcription, processing and degradation rates of genes by 4sU-seq (the Me ...
Download / Learn more Package Citations See dependency  

27,806

R Packages

239,283

Dependencies

73,837

Author Associations

27,807

Publication Badges

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