<i>adegenet</i>: a R package for the multivariate analysis of genetic markers

Abstract

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.

Keywords

R packageMultivariate statisticsSoftware packageSoftwareComputer scienceMultivariate analysisPopulationSoftware engineeringData miningProgramming languageMachine learning

Affiliated Institutions

Related Publications

GEIGER: investigating evolutionary radiations

Luke J. Harmon , Jason T. Weir , Chad D. Brock +2 more

Abstract Summary: GEIGER is a new software package, written in the R language, to describe evolutionary radiations. GEIGER can carry out simulations, parameter estimation and st...

2007 Bioinformatics 2491 citations

dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering

Tal Galili

Abstract Summary: dendextend is an R package for creating and comparing visually appealing tree diagrams. dendextend provides utility functions for manipulating dendrogram objec...

2015 Bioinformatics 1758 citations

Use of within-array replicate spots for assessing differential expression in microarray experiments

Gordon K. Smyth , Jean Michaud , Hamish S. Scott

The methodology is implemented in the limma software package for R, available from the CRAN repository http://www.r-project.org

2005 Computer applications in the biosciences 1400 citations

APE: Analyses of Phylogenetics and Evolution in R language

Emmanuel Paradis , Julien Claude , Korbinian Strimmer

Abstract Summary: Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics. APE provides both utilit...

2004 Bioinformatics 12200 citations

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

Emmanuel Paradis , Klaus Schliep

Abstract Summary After more than fifteen years of existence, the R package ape has continuously grown its contents, and has been used by a growing community of users. The releas...

2018 Bioinformatics 8399 citations

Publication Info

Year: 2008
Type: article
Volume: 24
Issue: 11
Pages: 1403-1405
Citations: 7558
Access: Closed

External Links

View on DOI.org

Social Impact

Altmetric

<i>adegenet</i>: a R package for the multivariate analysis of genetic markers

PlumX Metrics

Social media, news, blog, policy document mentions

Citation Metrics

7558

OpenAlex

Cite This

APA Style

                            
                                    Thibaut Jombart
                                
                            (2008). 
                            <i>adegenet</i>: a R package for the multivariate analysis of genetic markers. 
                            Bioinformatics
                            , 24
                            (11)
                            , 1403-1405.
                            https://doi.org/10.1093/bioinformatics/btn129

Identifiers

DOI: 10.1093/bioinformatics/btn129