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: |
2.1.1 |
| 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 |
| Suggests: |
pegas, hierfstat, akima, maps, splancs, tripack, testthat, poppr |
| Published: |
2018-02-02 |
| 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 <thibautjombart 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: |
Genetics |
| CRAN checks: |
adegenet results |