adegenet protocols

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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 2.1.1
Stability Stable
Requirements
methods, stats, parallel, utils, testthat, grDevices, ggplot2, MASS, reshape2, seqinr, R, igraph, ade4, shiny, akima, boot, ape, vegan, maps, spdep, dplyr, pegas, hierfstat, splancs, tripack, poppr
Maintained Yes

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Maintainer


  • person_outline Thibaut Jombart <>

Publications for adegenet

adegenet in pipelines

 (7)
2017
PMCID: 5415527
PMID: 28479988
DOI: 10.1002/ece3.2831

[…] ; rousset, ) using the g test, which computes the p‐value for the observed differences in frequencies between populations for all loci, using a markov chain algorithm. the r (r core team ) package, adegenet v1.6 (jombart & ahmed, ), was used to test for isolation by distance using a mantel test. lastly, we used the hierfstat package (goudet, ) in r to quantify genetic variation (f st) […]

2017
PMCID: 5552028
PMID: 28796789
DOI: 10.1371/journal.pntd.0005718

[…] v.1.1 []., to further explore population structure, discriminant analyses of principle components (dapc), principle component analyses (pca), and plots illustrating fst values were created using the adegenet package v. 2.0.2. [], available on r software v. 3.2.4 and rstudio v.0.99.893 []. dapc optimizes variation between clusters while minimizing variation within them. data are transformed using […]

2017
PMCID: 5655429
PMID: 29065114
DOI: 10.1371/journal.pone.0186488

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

2017
PMCID: 5744932
PMID: 29281653
DOI: 10.1371/journal.pone.0189234

[…] ii) the nuclear background shown by significant fst values., principal component analysis (pca) was used to further explore genetic differentiation between populations, using r 3.0.2 software [] and adegenet 1.3–9.2 package []. genetic structure among populations was additionally investigated using structure 2.3.3 []. a total of 106 simulations using 105 burn-in steps and mcmc (markov chain […]

2016
PMCID: 4765546
PMID: 26772770
DOI: 10.1093/aob/mcv191

[…] ‘fields’ () to calculate the geographic distance matrix among populations based on their gps coordinates. we then tested for the presence of isolation by distance each year with mantel tests in the ‘adegenet’ r package (), within each ecotype and on the whole data set. additionally, following the guidelines provided by , we regressed fst/(1 – fst) on the geographic distance., to better describe […]


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adegenet in publications

 (520)
PMCID: 5954203
DOI: 10.1128/mSystems.00205-17

[…] pca plots, including an additional principal component, did not detect clustering based on these factors (). we further performed discriminant analysis of principal components (dapc) using the adegenet package in r, and it confirmed the existence of separate clusters for tumor and normal samples (p < 2.2 × 10−16) (see ) but not for gender and tumor locations (p > 0.2 […]

PMCID: 5941068
PMID: 29739910
DOI: 10.1128/mBio.00381-18

[…] download text s1, docx file, 0.1 mb., random distribution of snps at linkage equilibrium. polymorphic site (snp) positions were analyzed using a monte carlo test implemented in the r package adegenet to determine if they are randomly distributed across chromosomes. the significance data are based on 500 replicates. density plots of representative chromosomes, which clearly indicated […]

PMCID: 5919407
PMID: 29698497
DOI: 10.1371/journal.pone.0196276

[…] population when adopting an approach without assumptions about hwe or linkage disequilibrium, discriminant analysis of principal component (dapc) was carried out with the method implemented in the adegenet package [] within the statistical package r version 3.3.2 []. dapc was conducted without a posteriori group assignments by inferring the most likely number of genetic clusters (k) using […]

PMCID: 5921550
PMID: 29699502
DOI: 10.1186/s12862-018-1173-6

[…] in []. these mean genotype estimates were used to calculate starting values of admixture proportions with the discriminant analysis of principal components (dapc) [] function in the r package adegenet [, ] for each respective number of clusters., the software entropy (like structure) uses multilocus genotype data to estimate admixture proportions given a number k of source populations. […]

PMCID: 5936904
PMID: 29765639
DOI: 10.1098/rsos.171615

[…] package in r []., we also directly tested hypotheses of population differentiation using multivariate analyses, specifically the discriminant analysis of principal components (dapc) in the r package adegenet []. dapc calculates principal components and then estimates a centroid and measures the variance for predefined populations. the discriminant analysis tests the probability […]


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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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