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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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Versioning


No version available

Documentation


Maintainer


  • person_outline Thibaut Jombart

Publications for adegenet

adegenet citations

 (675)
library_books

Interaction between Host MicroRNAs and the Gut Microbiota in Colorectal Cancer

2018
mSystems
PMCID: 5954203
DOI: 10.1128/mSystems.00205-17

[…] larly, 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 for all comparisons) () […]

library_books

Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen Pneumocystis

2018
MBio
PMCID: 5941068
PMID: 29739910
DOI: 10.1128/mBio.00381-18

[…] Name QD -filter “QD < 2.0.” Multisample variant call format (VCF) files were generated using FermiKit (). SNPs were annotated using snpEff (). Polymorphic site positions were analyzed using R package adegenet v.2.0.1 (). […]

call_split

Genetic structure of South African Nguni (Zulu) sheep populations reveals admixture with exotic breeds

2018
PLoS One
PMCID: 5919407
PMID: 29698497
DOI: 10.1371/journal.pone.0196276
call_split See protocol

[…] ch 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 the f […]

library_books

Admixture, evolution, and variation in reproductive isolation in the Boechera puberula clade

2018
BMC Evol Biol
PMCID: 5921550
PMID: 29699502
DOI: 10.1186/s12862-018-1173-6

[…] scribed 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. Due t […]

call_split

Structure and phylogeography of two tropical predators, spinner (Stenella longirostris) and pantropical spotted (S. attenuata) dolphins, from SNP data

2018
R Soc Open Sci
PMCID: 5936904
PMID: 29765639
DOI: 10.1098/rsos.171615
call_split See protocol

[…] aG 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 of each individual […]

library_books

Genome Wide Association Mapping of Seedling and Adult Plant Resistance to Barley Stripe Rust (Puccinia striiformis f. sp. hordei) in India

2018
Front Plant Sci
PMCID: 5928535
PMID: 29740461
DOI: 10.3389/fpls.2018.00520

[…] ng configuration, and a simulation of 106 cycles was applied. Cluster values (k) from 2 to 10 were chosen and 5 independent runs for each k were chosen to obtain consistent results. Additionally, the adegenet package for R statistical software (The R Development core team) was used to confirm the number of sub-populations by the Bayesian Information Criterion (BIC). Finally, on the base of PCA res […]

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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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