adegenet pipeline

adegenet specifications

Information


Unique identifier OMICS_11078
Name adegenet
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.0.0
Stability Stable
Requirements methods, ade4
Maintained Yes

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Documentation


Maintainer


  • person_outline Thibaut Jombart <>

Publications for adegenet

adegenet citations

 (5)
2018
PMCID: 5774298

[…] (jakobsson & rosenberg, 2007) to account for label switching artifacts and multimodality in each k tested. we summarized the genetic diversity using a principal component analysis (pca) in adegenet v2.0, which does not make assumptions of hwe and ld (jombart, 2008; jombart & ahmed, 2011). finally, we conducted a mantel test to evaluate isolation-by-distance (ibd) using […]

2017
PMCID: 5511155

[…] odds (po) >10 (strong selection p = 0.90), and a q-value < 0.05 for the false-discovery rate as the threshold settings. we conducted dapc and bca using the function dapc in the r55 package adegenet56, and we used structure 2.3.457 to discriminate genetic clusters. dapc is a “without a priori” method using partial synthetic variables to minimize variation within groups58, 59, whereas […]

2017
PMCID: 5655429

[…] was computed by 999 randomizations., jost’s measure of population differentiation (d) [56], pairwise nei’s gst [57] and pairwise fst [58] were estimated using the package mmod [59] implemented in adegenet [60], and hierfstat [61]. the mantel test [62] was performed using ade4 [63] implemented in mmod, with 999 permutations, to quantify associations between values of d, gst and fst obtained […]

2016
PMCID: 5322408

[…] assignment probabilities to the identified clusters: structure v. 2.3.4 (hubisz, falush, stephens, & pritchard, 2009) and discriminant analysis of principal components (dapcs) implemented in adegenet 2.01 (jombart, 2008). parameters used for structure were the following: 100,000 burn‐in length, 500,000 mcmc chain replicates, admixture model of ancestry and correlated allele frequencies. […]

2013
PMCID: 3779096

[…] al. 2010) as an alternative method to infer population subdivision. this multivariate method consists of a discriminant analysis on data transformed after a principal component analysis. we used the adegenet package (1.3-1) of the r 2.13.1 software (r foundation for statistical computing, vienna, austria, http://www.r-project.org) to perform dapc analyses. the k-means procedure implemented […]

adegenet institution(s)
MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College, London, UK; INSERM, CESP Centre for Research in Epidemiology and Population Health, U1018, Villejuif, France; Univ Paris-Sud, UMRS 1018, Villejuif, France
adegenet funding source(s)
ERC Grant (P33585) and NIGMS MIDAS Programme to Neil Ferguson

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