pegas: an R package for population genetics with an integrated-modular approach

By Emmanuel Paradis. Bioinform., 2010

2,343 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/0c0f0e71d733fb81047fdf52a37dd9810a4b6805

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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.”
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.”
The molecular biogeography of the Indo‐Pacific: Testing hypotheses with multispecies genetic patterns (2019, methodology): “AMOVA was conducted using the pegas package (Paradis, 2010) in R (R Core Team, 2014) for each dataset to estimate the variance components for individuals nested within sampling locations (s2 err ), sampling loca‐ tions nested within regions (s2 loc ), and regions (s2 reg ).”
Discriminant analysis of principal components: a new method for the analysis of genetically structured populations (2010, positive): “We hope that its implementation in the free software R [27], which hosts an ever increasing number of tools for population genetics and phylogenetics [38,52-54] will open new and exciting perspectives for the statistical analysis of genetic data.”
vcfr: a package to manipulate and visualize variant call format data in R (2017, methodology): “The package also includes functions to convert this information to formats used by existing R packages speciﬁcally designed to work with population genetic data [e.g. APE (Paradis et al. 2004), ADEGENET (Jombart 2008), PEGAS (Paradis 2010) and POPPR (Kamvar et al. 2014, 2015)].”
popart: full‐feature software for haplotype network construction (2015, methodology): “…in software packages such as TCS (Clement, Posada & Crandall 2000), NETWORK (http://www.ﬂuxus-engineering.com), SPLITSTREE (Huson & Bryant 2006) and PEGAS (Paradis 2010), and these methods have been used extensively in the literature ( TCS , Clement, Posada & Crandall 2000; Clement et al .”
StAMPP: an R package for calculation of genetic differentiation and structure of mixed‐ploidy level populations (2013, methodology): “StAMPP utilizes multithreading and matrix algebra to efficiently handle large-scale SNP data sets and improves on alternative software packages, such as adegenet (Jombart & Ahmed 2011), SPAGeDi (Hardy & Vekemans 2002), pegas (Paradis 2010), hierfstat (Goudet 2005), GenAlEx (Peakall & Smouse 2006) an”
GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update (2012, background): “For example, direct export is offered to programs such as GENEPOP (Rousset, 2008) and STRUCTURE (Pritchard et al. , 2000), and via these same formats to many other programs, including genetic packages in R such as adegenet (Jombart, 2008) and pegas (Paradis, 2010).”
PopGenReport: simplifying basic population genetic analyses in R (2014, methodology): “The genind data class has been adopted by several recently released packages including PEGAS (Paradis 2010), and MMOD (Winter 2012).”
Robust Identification of Local Adaptation from Allele Frequencies (2012, methodology): “Sets of neutral and selected SNPs were simulated as described above, and the differentiation statistics FST (using the pegas R library, Paradis, 2010), X TX and the related FLK (using an R script provided by the authors, Bonhomme et al., 2010) were calculated.”
adegenet 1.3-1: new tools for the analysis of genome-wide SNP data (2011, background): “…Team, 2011) is becoming a standard for the analysis of genetic data, offering a wealth of packages dedicated to population genetics (Jombart, 2008; Paradis, 2010), phylogenetics (Paradis et al., 2004; Schliep, 2011) or genome-wide association studies (Aulchenko et al., 2007; Clayton and Leung,…”