The DOI matches its Crossref record.
adegenet: a R package for the multivariate analysis of genetic markers
Abstract
Summary: The package adegenet for the R software is dedicated to the multivariate analysis of genetic markers. It extends the ade4 package of multivariate methods by implementing formal classes and functions to manipulate and analyse genetic markers. Data can be imported from common population genetics software and exported to other software and R packages. adegenet also implements standard population genetics tools along with more original approaches for spatial genetics and hybridization. Availability: Stable version is available from CRAN: http://cran.r-project.org/mirrors.html. Development version is available from adegenet website: http://adegenet.r-forge.r-project.org/. Both versions can be installed directly from R. adegenet is distributed under the GNU General Public Licence (v.2). Contact: jombart@biomserv.univ-lyon1.fr Supplementary information: Supplementary data are available at Bioinformatics online.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
No references could be resolved yet.
Research works printed but not linked: 14
- Chessel, 2004, The ade4 package-I-one-table methods, R News, 4, 5
- Dolédec, 1987, Rythmes saisonniers et composantes stationnelles en milieu aquatique, Acta Oecologica, Oecologia Generalis, 8, 403
- Dray, 2007, The ade4 package – II: two-table and K-table methods, R News, 7, 47
- Excoffier, 2006, Computer programs for population genetics data analysis: a survival guide, Nat. Rev. Genet, 7, 745, 10.1038/nrg1904 · DOI · Paper page
- Goudet, 2005, Hierfstat, a package for R to compute and test hierarchical F-statistics, Mol. Ecol. Notes, 5, 184, 10.1111/j.1471-8286.2004.00828.x · DOI · Paper page
- Goudet, 1996, Testing differentiation in diploid populations, Genetics, 144, 1933, 10.1093/genetics/144.4.1933 · DOI · Paper page
- Jombart, Revealing cryptic spatial patterns in genetic variability by a new multivariate method
- Laloë, 2007, Consensus genetic structuring and typological value of markers using multiple co-inertia analysis, Genet. Sel. Evol, 39, 545, 10.1186/1297-9686-39-5-545 · DOI
- Manel, 2003, Landscape genetics: combining landscape ecology and population genetics, Trends in Ecol. Evol, 18, 189, 10.1016/S0169-5347(03)00008-9 · DOI · Paper page
- Manni, 2004, Geographic patterns of (genetic, morphologic, linguistic) variation: how barriers can be detected by “Monmonier's algorithm”, Hum. Biol, 76, 173, 10.1353/hub.2004.0034 · DOI
- Monmonier, 1973, Maximum-difference barriers: an alternative numerical regionalization method, Geogr. Anal, 3, 245, 10.1111/j.1538-4632.1973.tb01011.x · DOI · Paper page
- Pritchard, 2000, Inference of population structure using multilocus genotype data, Genetics, 155, 945, 10.1093/genetics/155.2.945 · DOI · Paper page
- Raymond, 1995, Genepop (version 1.2): population genetics software for exact tests and ecumenicism, Journal of Heredity, 86, 248, 10.1093/oxfordjournals.jhered.a111573 · DOI · Paper page
- Warnes, 2003, The genetics package, R News, 3, 9
Cited by
Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil
Voloch, C. M., da Silva Francisco, R., de Almeida, L. G. P., Cardoso, C. C., Brustolini, O. J., Gerber, A. L., Guimarães, A. P. D. C., Mariani, D., da Costa, R. M., Ferreira, O. C., et al. (2021) · Journal of Virology · doi:10.1128/jvi.00119-21 · Cited by 372
Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil
Voloch, C. M., Silva F, R. D., de Almeida, L. G. P., Cardoso, C. C., Brustolini, O. J., Gerber, A. L., Guimarães, A. P. D. C., Mariani, D., Costa, R. M. D., Ferreira, O. C., et al. (2020) · doi:10.1101/2020.12.23.20248598 · Cited by 372
Genome Sequences Reveal Cryptic Speciation in the Human Pathogen Histoplasma capsulatum
Sepúlveda, V. E., Márquez, R., Turissini, D. A., Goldman, W. E., & Matute, D. R. (2017) · mBio · doi:10.1128/mbio.01339-17 · Cited by 175
Kaya, C., Generalovic, T. N., Ståhls, G., Hauser, M., Samayoa, A. C., Nunes-Silva, C. G., Roxburgh, H., Wohlfahrt, J., Ewusie, E. A., Kenis, M., et al. (2021) · BMC Biology · doi:10.1186/s12915-021-01029-w · Cited by 149
Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution
Kendall, M., & Colijn, C. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw124 · Cited by 134
Limited introgression supports division of giraffe into four species
Winter, S., Fennessy, J., & Janke, A. (2018) · Ecology and Evolution · doi:10.1002/ece3.4490 · Cited by 66
Barth, J. M. I., Damerau, M., Matschiner, M., Jentoft, S., & Hanel, R. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx067 · Cited by 62
Rhode, C., Badenhorst, R., Hull, K. L., Greenwood, M. P., Bester‐van der Merwe, A. E., Andere, A. A., Picard, C. J., & Richards, C. (2020) · Animal Genetics · doi:10.1111/age.12961 · Cited by 58
Elbrecht, V., Feld, C. K., Gies, M., Hering, D., Sondermann, M., Tollrian, R., & Leese, F. (2014) · Freshwater Science · doi:10.1086/674536 · Cited by 49
Patterns of Genetic Diversity and Mating Systems in a Mass-Reared Black Soldier Fly Colony
Hoffmann, L., Hull, K. L., Bierman, A., Badenhorst, R., Bester-van der Merwe, A. E., & Rhode, C. (2021) · Insects · doi:10.3390/insects12060480 · Cited by 45
High frequency of an otherwise rare phenotype in a small and isolated tiger population
Sagar, V., Kaelin, C. B., Natesh, M., Reddy, P. A., Mohapatra, R. K., Chhattani, H., Thatte, P., Vaidyanathan, S., Biswas, S., Bhatt, S., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2025273118 · Cited by 41
Kyle, C. J., Rico, Y., Castillo, S., Srithayakumar, V., Cullingham, C. I., White, B. N., & Pond, B. A. (2014) · Molecular Ecology · doi:10.1111/mec.12726 · Cited by 38
Mullins, J., McDevitt, A. D., Kowalczyk, R., Ruczyńska, I., Górny, M., & Wójcik, J. M. (2014) · Acta Theriologica · doi:10.1007/s13364-014-0180-2 · Cited by 34
Vergara, M., Cushman, S. A., & Ruiz-González, A. (2017) · Landscape Ecology · doi:10.1007/s10980-017-0512-0 · Cited by 29
Basto, M. P., Santos-Reis, M., Simões, L., Grilo, C., Cardoso, L., Cortes, H., Bruford, M. W., & Fernandes, C. (2016) · PLOS ONE · doi:10.1371/journal.pone.0145165 · Cited by 28
van der Ven, R. M., Flot, J.-F., Buitrago-López, C., & Kochzius, M. (2021) · Heredity · doi:10.1038/s41437-020-00379-5 · Cited by 26
Whole Genome Sequencing Reveals Signals of Adaptive Admixture in Creole Cattle
Ben-Jemaa, S., Adam, G., Boussaha, M., Bardou, P., Klopp, C., Mandonnet, N., & Naves, M. (2023) · Scientific Reports · doi:10.1038/s41598-023-38774-7 · Cited by 22
Samake, J. N., Lavretsky, P., Gunarathna, I., Follis, M., Brown, J. I., Ali, S., Yared, S., & Carter, T. E. (2023) · Molecular Ecology · doi:10.1111/mec.17136 · Cited by 22
Winter, D. J., Weir, B. S., Glare, T., Rhodes, J., Perrott, J., Fisher, M. C., Stajich, J. E., Digby, A., Dearden, P. K., & Cox, M. P. (2022) · iScience · doi:10.1016/j.isci.2022.105470 · Cited by 21
Wilk, A. J., Donlon, K. C., & Peterman, W. E. (2020) · Urban Ecosystems · doi:10.1007/s11252-020-00958-8 · Cited by 14
Díaz-Muñoz, C., Verce, M., De Vuyst, L., & Weckx, S. (2022) · iScience · doi:10.1016/j.isci.2022.105309 · Cited by 10
Genetic and Epigenetic Differentiation in Response to Genomic Selection for Avian Lay Date
Lindner, M., Verhagen, I., Mateman, A. C., van Oers, K., Laine, V. N., & Visser, M. E. (2024) · Evolutionary Applications · doi:10.1111/eva.13703 · Cited by 8
Population genetics of Bull Trout ( Salvelinus confluentus ) in the upper Athabasca River basin
Carroll, E. K. T., & Vamosi, S. M. (2021) · Ecology and Evolution · doi:10.1002/ece3.8110 · Cited by 3
Metadata
- Authors
- Jombart, T.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2008-04-08
- Volume
- 24
- Issue
- 11
- Pages
- 1403-1405
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2146290595
- Cited by
- 8,107
- References
- 0
- FWCI
- 18.28
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
