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.
| 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],
Zhian N. Kamvar
[aut, cre],
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],
Lindsay V. Clark
[ctb],
Pavel Dimens
[ctb] |
| 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 |
Documentation:
| Reference manual: | adegenet.pdf |
Downloads:
| Package source: | adegenet_2.1.10.tar.gz |
| Windows binaries: | r-devel: adegenet_2.1.10.zip, r-release: adegenet_2.1.10.zip, r-oldrel: adegenet_2.1.10.zip |
| macOS binaries: | r-release (arm64): adegenet_2.1.10.tgz, r-oldrel (arm64): adegenet_2.1.10.tgz, r-release (x86_64): adegenet_2.1.10.tgz, r-oldrel (x86_64): adegenet_2.1.10.tgz |
| Old sources: | adegenet archive |
Reverse dependencies:
| Reverse depends: | dartR, dartR.base, dartR.captive, dartR.data, dartR.popgen, dartR.sexlinked, dartR.sim, dartR.spatial, mmod, PopGenReport, poppr |
| Reverse imports: | adephylo, AlleleShift, apex, DA, graph4lg, hierfstat, snpAIMeR, SNPfiltR, StAMPP, treespace |
| Reverse suggests: | coreCollection, memgene, outbreaker2, pegas, polyRAD, polysat, quiddich, RAINBOWR, sequoia, vcfR, wingen |
Linking:
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