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adegenet  

Exploratory Analysis of Genetic and Genomic Data
View on CRAN: Click here


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

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

Install by package version:
library("remotes")
install_version("adegenet", "2.1.10")



Attach the package and use:
library("adegenet")
Maintained by
Zhian N. Kamvar
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2007-04-11
Latest Update: 2023-01-26
Description:
Toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure ('genind' class), alleles counts by populations ('genpop'), and genome-wide SNP data ('genlight'). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods.
How to cite:
Zhian N. Kamvar (2007). adegenet: Exploratory Analysis of Genetic and Genomic Data. R package version 2.1.10, https://cran.r-project.org/web/packages/adegenet
Previous versions and publish date:
1.0-0 (2007-04-11 10:21), 1.0-1 (2007-08-25 18:47), 1.0-2 (2007-09-10 10:14), 1.1-0 (2008-02-13 21:20), 1.1-1 (2008-04-18 20:17), 1.1-2 (2008-06-02 14:08), 1.2-0 (2008-07-08 19:14), 1.2-1 (2008-08-01 15:01), 1.2-2 (2008-12-19 11:55), 1.2-3 (2009-04-03 11:41), 1.2-4 (2010-04-16 18:03), 1.2-5 (2010-07-29 11:13), 1.2-6 (2010-09-22 21:36), 1.2-7 (2010-10-29 10:24), 1.2-8 (2010-11-04 20:54), 1.3-0 (2011-06-24 18:57), 1.3-1 (2011-09-14 21:21), 1.3-2 (2011-11-10 14:37), 1.3-3 (2011-12-23 06:54), 1.3-4 (2012-01-18 21:50), 1.3-5 (2012-11-01 21:38), 1.3-6 (2013-01-29 21:31), 1.3-7 (2013-04-06 21:51), 1.3-8 (2013-05-15 18:54), 1.3-9.1 (2013-08-09 14:23), 1.3-9.2 (2013-08-10 00:57), 1.3-9 (2013-06-04 18:08), 1.4-0 (2014-03-14 15:29), 1.4-1 (2014-03-18 18:20), 1.4-2 (2014-05-13 07:44), 2.0.0 (2015-07-07 15:44), 2.0.1 (2016-02-15 16:12), 2.1.0 (2017-10-12 21:20), 2.1.1 (2018-02-02 19:21), 2.1.2 (2020-01-20 20:50), 2.1.3 (2020-05-11 00:00), 2.1.4 (2021-07-17 20:00), 2.1.5 (2021-10-09 20:20), 2.1.6 (2022-05-15 22:40), 2.1.7 (2022-06-06 22:10), 2.1.8 (2022-10-02 17:30), 2.1.9 (2023-01-12 14:00)
Other packages that cited adegenet R package
View adegenet citation profile
Other R packages that adegenet depends, imports, suggests or enhances
Functions, R codes and Examples using the adegenet R package
Some associated functions: AIC.snapclust . AICc . BIC.snapclust . H3N2 . HWE . Hs . Hs.test . KIC . SNPbin . accessors . adegenet.package . as-methods . as.SNPbin . as.genlight . ascore . auxil . chooseCN . colorplot . compoplot . coords.monmonier . dapc . dapcGraphics . dapcIllus . df2genind . dist.genpop . doc_C_routines . eHGDP . export_to_mvmapper . fasta2DNAbin . fasta2genlight . find.clusters . gengraph . genind . genind2df . genind2genpop . genlight . genpop . glAux . glPca . glPlot . glSim . haploGen . hierarchy-methods . hybridize . hybridtoy . import2genind . inbreeding . isPoly . loadingplot . makefreq . microbov . minorAllele . monmonier . mutations . nancycats . new.genind . new.genpop . old2new . pairDist . population-methods . propShared . propTyped . read.PLINK . read.fstat . read.genepop . read.genetix . read.snp . read.structure . repool . rupica . scaleGen . selpopsize . seploc . seppop . seqTrack . sequences . servers . showmekittens . sim2pop . snapclust.choose.k . snapclust . snpposi . spca . spca.rtests . spcaIllus . spca_randtest . strata-methods . swallowtails . tab . truenames . virClasses . web . xvalDapc . 
Some associated R codes: AIC.snapclust.R . AICc.snapclust.R . BIC.snapclust.R . HWE.R . Hs.R . KIC.snapclust.R . PCtest.R . SNPbin.R . accessors.R . adegenet.package.R . auxil.R . basicMethods.R . chooseCN.R . classes.R . colorplot.R . compoplot.R . constructors.R . coords.monmonier.R . dapc.R . datasets.R . dist.genlight.R . dist.genpop.R . doc_C_routines.R . export.R . export_to_mvmapper.R . find.clust.R . fstat.R . gengraph.R . genind2genpop.R . glFunctions.R . glHandle.R . glPlot.R . glSim.R . global_local_tests.R . gstat.randtest.R . handling.R . haploGen.R . haploPop.R . hierarchyMethods.R . hybridize.R . import.R . inbreeding.R . loadingplot.R . makefreq.R . minorAllele.R . monmonier.R . mutations.R . old2new.R . orthobasis.R . pairDist.R . propShared.R . propTyped.R . scale.R . seqTrack.R . sequences.R . servers.R . setAs.R . showmekittens.R . simOutbreak.R . snapclust.R . snapclust.choose.k.R . snpposi.R . snpzip.R . spca.R . spca_randtest.R . strataMethods.R . xvalDapc.R . zzz.R .  Full adegenet package functions and examples
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