adegenet

Exploratory Analysis of Genetic and Genomic Data

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.

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Description file content

Package
adegenet
Version
2.1.0
Encoding
UTF-8
Title
Exploratory Analysis of Genetic and Genomic Data
Author
Thibaut Jombart, Zhian N. Kamvar, Caitlin Collins, Roman Lustrik, Marie- Pauline Beugin, Brian J. Knaus, Peter Solymos, Vladimir Mikryukov, Klaus Schliep, Tiago Maié, Libor Morkovsky, Ismail Ahmed, Anne Cori, Federico Calboli, RJ Ewing
Maintainer
Thibaut Jombart
Suggests
pegas, hierfstat, akima, maps, splancs, tripack, testthat, poppr
Depends
R (>= 2.14), methods, ade4
Imports
utils, stats, grDevices, MASS, igraph, ape, shiny, ggplot2, seqinr, parallel, spdep, boot, reshape2, dplyr (>= 0.4.1), vegan
URL
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.
Collate
adegenet.package.R datasets.R dist.genlight.R orthobasis.R classes.R constructors.R accessors.R basicMethods.R handling.R auxil.R minorAllele.R setAs.R SNPbin.R strataMethods.R hierarchyMethods.R glHandle.R glFunctions.R glSim.R find.clust.R hybridize.R scale.R fstat.R import.R seqTrack.R chooseCN.R genind2genpop.R loadingplot.R sequences.R gstat.randtest.R makefreq.R colorplot.R monmonier.R spca.R coords.monmonier.R haploGen.R old2new.R global_local_tests.R dapc.R compoplot.R xvalDapc.R haploPop.R PCtest.R dist.genpop.R Hs.R propShared.R export.R HWE.R propTyped.R inbreeding.R glPlot.R gengraph.R simOutbreak.R mutations.R snpposi.R snpzip.R pairDist.R snapclust.R AIC.snapclust.R AICc.snapclust.R BIC.snapclust.R KIC.snapclust.R snapclust.choose.k.R servers.R showmekittens.R spca_randtest.R export_to_mvmapper.R doc_C_routines.R zzz.R
License
GPL (>= 2)
LazyLoad
yes
RoxygenNote
6.0.1
NeedsCompilation
yes
Packaged
2017-10-12 15:31:47 UTC; thibaut
Repository
CRAN
Date/Publication
2017-10-12 19:20:52 UTC

install.packages('adegenet')

2.1.0

2 months ago

https://github.com/thibautjombart/adegenet

Thibaut Jombart

GPL (>= 2)

Depends on

R (>= 2.14), methods, ade4

Imports

utils, stats, grDevices, MASS, igraph, ape, shiny, ggplot2, seqinr, parallel, spdep, boot, reshape2, dplyr (>= 0.4.1), vegan

Suggests

pegas, hierfstat, akima, maps, splancs, tripack, testthat, poppr

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