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.
| Version: |
2.1.10 |
| Depends: |
R (≥ 2.14), methods, ade4 |
| Imports: |
utils, stats, grDevices, MASS, igraph, ape, shiny, ggplot2, seqinr, parallel, boot, reshape2, dplyr (≥ 0.4.1), vegan |
| Suggests: |
adespatial, pegas, hierfstat, maps, spdep, interp, splancs, poppr, testthat |
| Published: |
2023-01-26 |
| DOI: |
10.32614/CRAN.package.adegenet |
| Author: |
Thibaut Jombart 
[aut] (<https://orcid.org/0000-0003-2226-8692>),
Zhian N. Kamvar
[aut, cre] (<https://orcid.org/0000-0003-1458-7108>),
Caitlin Collins [ctb],
Roman Lustrik [ctb],
Marie-Pauline Beugin [ctb],
Brian J. Knaus [ctb],
Peter Solymos [ctb],
Vladimir Mikryukov [ctb],
Klaus Schliep [ctb],
Tiago Maié [ctb],
Libor Morkovsky [ctb],
Ismail Ahmed [ctb],
Anne Cori [ctb],
Federico Calboli [ctb],
RJ Ewing [ctb],
Frédéric Michaud [ctb],
Rebecca DeCamp [ctb],
Alexandre Courtiol
[ctb]
(<https://orcid.org/0000-0003-0637-2959>),
Lindsay V. Clark
[ctb] (<https://orcid.org/0000-0002-3881-9252>),
Pavel Dimens
[ctb] (<https://orcid.org/0000-0003-3823-0373>) |
| Maintainer: |
Zhian N. Kamvar <zkamvar at gmail.com> |
| License: |
GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| URL: |
https://github.com/thibautjombart/adegenet |
| NeedsCompilation: |
yes |
| Citation: |
adegenet citation info |
| Materials: |
README ChangeLog |
| In views: |
Epidemiology |
| CRAN checks: |
adegenet results |