Linking genomics and population genetics with R

vcfr: a package to manipulate and visualize variant call format data in R

(2016) Brian J. Knaus et al.   Molecular Ecology Resources

A vision for ubiquitous sequencing

(2015) Yaniv Erlich   GENOME RESEARCH

Population genomic analysis uncovers African and European admixture inDrosophila melanogasterpopulations from the south-eastern United States and Caribbean Islands

(2015) Joyce Y. Kao et al.   MOLECULAR ECOLOGY

A genomewide catalogue of single nucleotide polymorphisms in white-beaked and Atlantic white-sided dolphins

(2015) R. Fernández et al.   Molecular Ecology Resources

Accounting for genotype uncertainty in the estimation of allele frequencies in autopolyploids

(2015) Paul D. Blischak et al.   Molecular Ecology Resources

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

Accounting for uncertainty in DNA sequencing data

(2015) Jason A. O’Rawe et al.   TRENDS IN GENETICS

argyle: An R Package for Analysis of Illumina Genotyping Arrays

(2015) Andrew P. Morgan   G3-Genes Genomes Genetics

Big Data: Astronomical or Genomical?

(2015) Zachary D. Stephens et al.   PLOS BIOLOGY

VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants

(2014) V. Obenchain et al.   BIOINFORMATICS

poRe: an R package for the visualization and analysis of nanopore sequencing data

(2014) Mick Watson et al.   BIOINFORMATICS

A field guide to whole-genome sequencing, assembly and annotation

(2014) Robert Ekblom et al.   Evolutionary Applications

Recent novel approaches for population genomics data analysis

(2014) Kimberly R. Andrews et al.   MOLECULAR ECOLOGY

Fast Principal Component Analysis of Large-Scale Genome-Wide Data

(2014) Gad Abraham et al.   PLoS One

Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, Highly-Repetitive Transposable Elements

(2014) Rajiv C. McCoy et al.   PLoS One

Scalable Genomics with R and Bioconductor

(2014) Michael Lawrence et al.   STATISTICAL SCIENCE

Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction

(2014) Zhian N. Kamvar et al.   PeerJ

Calculation of Tajima’s D and other neutrality test statistics from low depth next-generation sequencing data

(2013) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Genotyping-by-sequencing in ecological and conservation genomics

(2013) Shawn R. Narum et al.   MOLECULAR ECOLOGY

Genome sequencing and population genomics in non-model organisms

(2013) Hans Ellegren   TRENDS IN ECOLOGY & EVOLUTION

mmod: an R library for the calculation of population differentiation statistics

(2012) David J. Winter   Molecular Ecology Resources

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs

(2011) H. E. L. Lischer et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

adegenet 1.3-1: new tools for the analysis of genome-wide SNP data

(2011) Thibaut Jombart et al.   BIOINFORMATICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

Finding Structure with Randomness: Probabilistic Algorithms for Constructing Approximate Matrix Decompositions

(2011) N. Halko et al.   SIAM REVIEW

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

(2010) E. Paradis   BIOINFORMATICS

Discriminant analysis of principal components: a new method for the analysis of genetically structured populations

(2010) Thibaut Jombart et al.   BMC GENETICS

R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips

(2009) M. E. Ritchie et al.   BIOINFORMATICS

Genetic markers in the playground of multivariate analysis

(2009) T Jombart et al.   HEREDITY

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

(2008) Thibaut Jombart   BIOINFORMATICS

Correlation-Based Inference for Linkage Disequilibrium With Multiple Alleles

(2008) D. V. Zaykin et al.   GENETICS

Revealing cryptic spatial patterns in genetic variability by a new multivariate method

(2008) T Jombart et al.   HEREDITY

Estimation of Nucleotide Diversity, Disequilibrium Coefficients, and Mutation Rates from High-Coverage Genome-Sequencing Projects

(2008) M. Lynch   MOLECULAR BIOLOGY AND EVOLUTION