adegenet: a R package for the multivariate analysis of genetic markers

By Thibaut Jombart. Bioinform., 2008

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View Paper: https://www.semanticscholar.org/paper/b88d13597ee90d5f6bdc33c85ae52e1de9e3fd0a

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In Genetics

Citations in the corpus

PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R (2014, background): “However, these tend to specialize on specific subsets of analyses (e.g., Vilella 2005; Rozas et al. 2001; Purcell et al. 2007; Jombart 2008; Paradis 2010) or cannot process whole-genome data (e.”
adegenet 1.3-1: new tools for the analysis of genome-wide SNP data (2011, methodology): “In this article, we introduce new tools implemented in the R package adegenet (Jombart, 2008) which ∗ To whom correspondence should be addressed. allow large genomic datasets (e.g. hundreds of individuals typed for hundreds of thousands SNPs) to be analyzed using standard personal computers.”
Recent responses to climate change reveal the drivers of species extinction and survival (2020, methodology): “, historical, absolute change, and rate of change) using the R package adegenet (42), after scaling each variable, and retaining the number of principal components associated with an optimal alpha score (using the optim.”
Ecologically differentiated stress-tolerant endosymbionts in the dinoflagellate genus Symbiodinium (Dinophyceae) Clade D are different species (2014, methodology): “Calculations of genetic (Euclidian) distance between genotypes (Jombart 2008) and Bayesian analysis of 227 MLGs using the program STRUCTURE (Pritchard et al. 2000) identified three reproductively isolated populations (K ¼ 3, Figs 7, 8, S10 and S11), each corresponding to phylogenetic groupings…”
Principal Component Analysis on Spatial Data: An Overview (2013, positive): “…is reported in and its output visualized using functions provided in Charlton et al. (2010). the R (Ihaka and Gentlemen 1996) adeganet package (Jombart 2008), where its application in related re PCA with Spatial Autocorrelation search areas, such as those found in ecology, should be…”
mmod: an R library for the calculation of population differentiation statistics (2012, methodology): “Modern measures of differentiation ( MMOD ) is an R library that integrates with ADEGENET and allows the calculation of these statistics from standard population genetic ﬁles.”
Standard methods for characterising subspecies and ecotypes of Apis mellifera (2013, methodology): “Currently there are studies underway with the methods in GENELAND (Guillot, 2005) and TESS (Durand, 2009), two software packages based on Bayesian assignment, and in ADEGENET (Jombart, 2008), a PCA based software package in the Statistical language R.”
Spider: An R package for the analysis of species identity and evolution, with particular reference to DNA barcoding (2012, methodology): “S PIDER requires the installation of the packages APE (Paradis et al. 2004), PEGAS (Paradis 2010), ADEGENET (Jombart 2008) and MASS (Venables & Ripley 2002), which provide the primary data structures for working with DNA sequences and phylogenetic trees.”
Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality (2015, methodology): “To demonstrate calculating a dendrogram with bootstrap support, we used the poppr function aboot on population allelic frequencies derived from the data set microbov in the adegenet package with 1000 bootstrap replicates (Laloë et al., 2007; Jombart, 2008).”
PopGenReport: simplifying basic population genetic analyses in R (2014, methodology): “PCOA ) included in the POPGENREPORT function are derived from, or build upon, analyses that were initially developed by Jombart (2008).”
Climate change induced hybridization in flying squirrels (2010, methodology): “We plotted each species and the hybrids identified in the STRUCTURE analyses and 95% confidence ellipses around them.”
dartr: An r package to facilitate analysis of SNP data generated from reduced representation genome sequencing (2018, background): “In many cases, this involves import to a genind object (Jombart, 2008), then conversion to a genlight object.”
Maintaining tiger connectivity and minimizing extinction into the next century: Insights from landscape genetics and spatially-explicit simulations (2017, methodology): “At the end of each simulation, we calculated genetic diversity indices (heterozygosity, inbreeding and allelic richness) and differentiation indices (Global and pairwise Fst, G’st, Jost D) (Jombart 2008; Adamack & Gruber 2014).”
Directional genetic differentiation and relative migration (2013, neutral): “2000), ADEGENET (Jombart 2008), or DAPC (Jombart et al.”
pegas: an R package for population genetics with an integrated-modular approach (2010, methodology): “It requires a standard R installation as well as two packages: ape (Paradis et al. , 2004) and adegenet (Jombart, 2008).”
Discriminant analysis of principal components: a new method for the analysis of genetically structured populations (2010, neutral): “K inferred by STRUCTURE 6 ([2,7]) 3 ([2,6]) 2 ([2,2]) 2 ([2,5])”
Restriction site‐associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference (2015, neutral): “3-7 (Jombart 2008), ape_3.”